PaperBLAST
PaperBLAST Hits for reanno::PS:Dsui_0519 Methylmalonyl-CoA mutase (EC 5.4.99.2) (Dechlorosoma suillum PS) (721 a.a., MSADASKPQL...)
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>reanno::PS:Dsui_0519 Methylmalonyl-CoA mutase (EC 5.4.99.2) (Dechlorosoma suillum PS)
MSADASKPQLPNSDNLDAWAKAAAKSAPGGDVNALNWITPEGLTVKPLYTKKDVEDLPYA
DTLPGFAPYLRGPQATMYAVRPWTIRQYAGFSTAEESNAFYRKALAAGGQGVSVAFDLAT
HRGYDSDNPRVLGDVGKAGVAIDSVEDMKILFDGIPLDKISVSMTMNGAVLPILAGYIVA
AEEQGVSQEQLSGTIQNDILKEFMVRNTYIYPPKPSMKIISDIFGYTAQHMPKFNSISIS
GYHIQEAGANQAIELAFTLADGMEYVRTGIASGLDVDAFAGRLSFFWAVGMNFYLEIAKM
RAGRMLWHRIMSQFNPKSAKSLMLRTHSQTSGWSLTEQDPYNNVVRTTIEAMAAVFGGTQ
SLHTNALDEAIALPTEFSARIARNTQLIIQEETHICNVVDPWAGSYMMEKLTQDMADKAW
SIIQEIEAMGGMTKAVESGWAKMQVETCAADKQARIDSGKDVIVGVNKYKLAKEDQIDIL
DIDNHAVREAQIARLKKIRASRDSAAVQAALDALTQCAESGEGNLLDLSVKAIRLRATVG
EVSDALEKVFGRFRANNQTISGVYGGVVEGQESWESIKADIAKFAEEEGRRPRIMIAKLG
QDGHDRGAKVVATAFADLGFDIDMGPLFQTPEEAARQAVENDVHAIGVSSLAAGHKTLLP
ALVNSLKEQGADDIIVFAGGVIPAQDYDTLYAAGAKAIFGPGTRIEDSAKRVLEEIRKSR
G
Running BLASTp...
Found 170 similar proteins in the literature:
Dsui_0519 Methylmalonyl-CoA mutase (EC 5.4.99.2) from Dechlorosoma suillum PS
100% identity, 100% coverage
- mutant phenotype: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (METHYLMALONYL-COA-MUT-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
CAP2UW1_1139 methylmalonyl-CoA mutase, large subunit from Candidatus Accumulibacter phosphatis clade IIA str. UW-1
84% identity, 98% coverage
Pnuc_0910 methylmalonyl-CoA mutase from Polynucleobacter sp. QLW-P1DMWA-1
77% identity, 96% coverage
mcmA / Q3J4D7 methylmalonyl-CoA mutase (EC 5.4.99.2) from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (see paper)
MCM_CERS4 / Q3J4D7 Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (Rhodobacter sphaeroides) (see 2 papers)
RSP_2192 Methylmalonyl-CoA mutase from Rhodobacter sphaeroides 2.4.1
70% identity, 98% coverage
- function: Radical enzyme that catalyzes the transformation of (2R)- methylmalonyl-CoA to succinyl-CoA. Is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation required for R.sphaeroides growth on acetate as sole carbon source.
catalytic activity: (R)-methylmalonyl-CoA = succinyl-CoA (RHEA:22888)
cofactor: adenosylcob(III)alamin
subunit: Homodimer. - Acrylyl-coenzyme A reductase, an enzyme involved in the assimilation of 3-hydroxypropionate by Rhodobacter sphaeroides
Asao, Journal of bacteriology 2013 - “...by RSP_0812), and (2R)-methylmalonyl-CoA mutase (encoded by RSP_2192). the gene (RSP_1434) encoding a member of the medium-chain dehydrogenase/reductase (MDR)...”
- In vivo analysis of cobinamide salvaging in Rhodobacter sphaeroides strain 2.4.1
Gray, Journal of bacteriology 2009 - “...acetate (MeaA, locus tag RSP_0961; McmA, locus tag RSP_2192, respectively) (1, 22, 23), methionine synthase (MetH, locus tag RSP_3346) (16), glutamate mutase...”
Glov_3260 methylmalonyl-CoA mutase, large subunit from Geobacter lovleyi SZ
70% identity, 98% coverage
Pden_3681 methylmalonyl-CoA mutase, large subunit from Paracoccus denitrificans PD1222
PDEN_RS18265 methylmalonyl-CoA mutase from Paracoccus denitrificans PD1222
70% identity, 98% coverage
LIC20209 methylmalonyl-COA mutase large subunit from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
68% identity, 96% coverage
LB274 methylmalonyl-CoA mutase from Leptospira interrogans serovar lai str. 56601
67% identity, 96% coverage
D3ZKG1 Methylmalonyl-CoA mutase, mitochondrial from Rattus norvegicus
66% identity, 84% coverage
- Gephyrin Interacts with the K-Cl Cotransporter KCC2 to Regulate Its Surface Expression and Function in Cortical Neurons
Al, The Journal of neuroscience : the official journal of the Society for Neuroscience 2022 (secret) - The mitochondrial proteomic changes of rat hippocampus induced by 28-day simulated microgravity.
Ji, PloS one 2022 - “...subunit beta, mitochondrial 1.60 0.002549 G3V7I5_RAT G3V7I5 Aldh1b1 Aldehyde dehydrogenase X, mitochondrial 1.60 0.006674 D3ZKG1_RAT D3ZKG1 Mmut Methylmalonyl CoA mutase 1.60 0.015932 F210A_RAT Q5XIJ4 Fam210a Protein FAM210A 1.60 0.013908 FMT_RAT Q5I0C5 Mtfmt Methionyl-tRNA formyltransferase, mitochondrial 1.60 0.018123 CEGT_RAT Q9R0E0 Ugcg Ceramide glucosyltransferase 1.60 0.020969 A0A0H2UI21_RAT A0A0H2UI21...”
- Preconditioning With Intermittent Hypobaric Hypoxia Attenuates Stroke Damage and Modulates Endocytosis in Residual Neurons.
Wan, Frontiers in neurology 2021 - “...Q4QQS3 14 Nipsnap homolog 3B Nipsnap3b 0.508148532 0.976677836 Q5M949 15 Methylmalonyl-CoA mutase Mut 0.64085441 0.641931454 D3ZKG1 16 Mitochondrial pyruvate carrier 1 Mpc1 0.638965701 0.646189605 P63031 17 U6 snRNA-associated Sm-like protein LSm2 Lsm2 0.653782363 0.613117637 Q6MG66 18 Laminin subunit gamma 1 Lamc1 0.635544098 0.653935863 F1MAA7 19 Haloacid...”
- Mechanisms of acute kidney injury induced by experimental Lonomia obliqua envenomation.
Berger, Archives of toxicology 2015 - “...regulates blood pressure/ Its inhibition decreases the production of NO. Caplin et al. , 2012 D3ZKG1 Methylmalonyl- CoA mutase, mitochondrial (Mut) 2.55 0.05 Involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle/ Knockout mouse for...”
2xiqA / P22033 Crystal structure of human methylmalonyl-coa mutase in complex with adenosylcobalamin and malonyl-coa (see paper)
66% identity, 97% coverage
- Ligands: cobalamin; malonyl-coenzyme a (2xiqA)
B7Q1G1 methylmalonyl-CoA mutase from Ixodes scapularis
66% identity, 94% coverage
MUT / P22033 Methylmalonyl-CoA mutase, mitochondrial (EC 5.4.99.2) from Homo sapiens (see 4 papers)
MUTA_HUMAN / P22033 Methylmalonyl-CoA mutase, mitochondrial; MCM; Methylmalonyl-CoA isomerase; EC 5.4.99.2 from Homo sapiens (Human) (see 31 papers)
P22033 methylmalonyl-CoA mutase (EC 5.4.99.2) from Homo sapiens (see 6 papers)
NP_000246 methylmalonyl-CoA mutase, mitochondrial precursor from Homo sapiens
66% identity, 93% coverage
- function: Catalyzes the reversible isomerization of methylmalonyl-CoA (MMCoA) (generated from branched-chain amino acid metabolism and degradation of dietary odd chain fatty acids and cholesterol) to succinyl-CoA (3-carboxypropionyl-CoA), a key intermediate of the tricarboxylic acid cycle.
catalytic activity: (R)-methylmalonyl-CoA = succinyl-CoA (RHEA:22888)
cofactor: adenosylcob(III)alamin
subunit: Homodimer (PubMed:20876572). Interacts (the apoenzyme form) with MMAA; the interaction is GTP dependent (PubMed:20876572, PubMed:21138732, PubMed:28943303). - Genetic analysis of isolated methylmalonic acidemia in Henan, China: c.1663G>A variant of MMUT prevalent in the Henan population.
Guo, Clinica chimica acta; international journal of clinical chemistry 2024 (PubMed)- GeneRIF: Genetic analysis of isolated methylmalonic acidemia in Henan, China: c.1663G>A variant of MMUT prevalent in the Henan population.
- Naturally occurring cobalamin (B12) analogs can function as cofactors for human methylmalonyl-CoA mutase.
Sokolovskaya, Biochimie 2021 - GeneRIF: Naturally occurring cobalamin (B12) analogs can function as cofactors for human methylmalonyl-CoA mutase.
- Delineating the clinical spectrum of isolated methylmalonic acidurias: cblA and mut.
Hörster, Journal of inherited metabolic disease 2021 (PubMed)- GeneRIF: Delineating the clinical spectrum of isolated methylmalonic acidurias: cblA and mut.
- A rare mutation c.1663G > A (p.A555T) in the MMUT gene associated with mild clinical and biochemical phenotypes of methylmalonic acidemia in 30 Chinese patients.
Liang, Orphanet journal of rare diseases 2021 - GeneRIF: A rare mutation c.1663G > A (p.A555T) in the MMUT gene associated with mild clinical and biochemical phenotypes of methylmalonic acidemia in 30 Chinese patients.
- A novel small molecule approach for the treatment of propionic and methylmalonic acidemias.
Armstrong, Molecular genetics and metabolism 2021 - GeneRIF: A novel small molecule approach for the treatment of propionic and methylmalonic acidemias.
- Different mutations in the MMUT gene are associated with the effect of vitamin B12 in a cohort of 266 Chinese patients with mut-type methylmalonic acidemia: A retrospective study.
Yu, Molecular genetics & genomic medicine 2021 - GeneRIF: Different mutations in the MMUT gene are associated with the effect of vitamin B12 in a cohort of 266 Chinese patients with mut-type methylmalonic acidemia: A retrospective study.
- Pre-implantation genetic diagnosis in an Iranian family with a novel mutation in MUT gene.
Habibzadeh, BMC medical genetics 2020 - GeneRIF: Our study identified a novel, deleterious, heterozygous missense mutation in MUT gene in a couple and helps to consider the genetic counselling and prenatal diagnosis more seriously for this family with clinical phenotypes of organic acidemia.
- Proteomics Reveals that Methylmalonyl-CoA Mutase Modulates Cell Architecture and Increases Susceptibility to Stress.
Costanzo, International journal of molecular sciences 2020 - GeneRIF: Proteomics Reveals that Methylmalonyl-CoA Mutase Modulates Cell Architecture and Increases Susceptibility to Stress.
- More
- Using metabolic abnormalities of carriers in the neonatal period to evaluate the pathogenicity of variants of uncertain significance in methylmalonic acidemia
Xiao, Frontiers in genetics 2024 - “.../ MMACHC FASTA sequences were retrieved from the UniProt website ( https://www.UniProt.org/ ; MMUT ID: P22033; MMACHC ID: Q9Y4U1). The associated protein sequences were retrieved using the SnapGene tool. Damaged coding non-synonymous SNPs (nsSNPs) were examined to determine whether the protein in question was functional. The...”
- Methylmalonic acidemia triggers lysosomal-autophagy dysfunctions.
Costanzo, Cell & bioscience 2024 - “...library. For the targeted assay, 12 unique peptides/precursors of human methylmalonyl-CoA mutase, mitochondrial (UniProt accession: P22033) were exported as inclusion list from Skyline for unscheduled or scheduled targeted PRM analysis. Tryptic peptides (2g) of the corresponding samples were measured using an Ultimate 3000 nano RSLC system...”
- Proteomics Reveals that Methylmalonyl-CoA Mutase Modulates Cell Architecture and Increases Susceptibility to Stress
Costanzo, International journal of molecular sciences 2020 - “...identified by LFQ proteomics in MUT-KO. UniProt Accession Protein Name Gene Name Regulation Log2 Difference P22033 Methylmalonyl-CoA mutase, mitochondrial MUT DOWN 8.4 P23434 Glycine cleavage system H protein, mitochondrial GCSH DOWN 3.8 Q99595 Mitochondrial import inner membrane translocase subunit Tim17-A TIMM17A DOWN 3.3 Q8N4T8 Carbonyl reductase...”
- Brain Proteomic Profiling in Intractable Epilepsy Caused by TSC1 Truncating Mutations: A Small Sample Study.
Liu, Frontiers in neurology 2020 - “...1.76 Early endosome membrane/Recycling endosome membrane Q9BZ23 Pantothenate kinase 2, mitochondrial (PANK2) 0.038373648 1.8 Mitochondrion/Cytoplasm P22033 Methylmalonyl-CoA mutase, mitochondrial (MMUT) 0.016470242 1.8 Mitochondrion matrix Q9Y2K5 R3H domain-containing protein 2 (R3HDM2) 0.03788905 1.85 Nucleus O75694 Nuclear pore complex protein Nup155 (NUP155) 0.043543604 1.86 Nucleus/ Nucleus membrane Q9H9A6...”
- How haptophytes microalgae mitigate vitamin B12 limitation
Nef, Scientific reports 2019 - “.... thaliana SAHH (P23526; O23255), Rattus norvegicus CBLA (D3ZNY3), Homo sapiens CBLB (Q96EY8) and MMCM (P22033), Propionibacterium freudenreichii subsp. shermanii MMCM (P11653). Homologous genes identified this way were searched again in T . lutea genome using TBlastX (expected threshold 1E-1). Conserved functional domains were identified by...”
- Proteomic analysis reveals dysregulated cell signaling in ejaculated spermatozoa from infertile men.
Samanta, Asian journal of andrology 2019 - “...domain-containing protein 1 isoform 1 Q5TCS8 221 3.3 39.0 58.3 58.7 Methylmalonyl-CoA mutase, mitochondrial precursor P22033 83 3.3 10.3 11.7 16.0 Sorting and assembly machinery component 50 homolog Q9Y512 52 3.3 5.7 10.7 18.3 Choline dehydrogenase, mitochondrial Q8NE62 65 3.7 13.3 15.0 24.7 Cytochrome b5 domain-containing...”
- Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas.
Drendel, Clinical proteomics 2018 - “...0.01 Q9Y619 Mitochondrial ornithine transporter 1 (Solute carrier family 25 member 15) 0.22 1.21 0.01 P22033 Methylmalonyl-CoA mutase, mitochondrial (MCM) (EC 5.4.99.2) (Methylmalonyl-CoA isomerase) 0.60 0.76 0.01 P20674 Cytochrome c oxidase subunit 5A, mitochondrial (Cytochrome c oxidase polypeptide Va) 0.80 0.77 0.01 Q15111 Inactive phospholipase C-like...”
- Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants
Ghoraba, Meta gene 2015 - “..., Escherichia coli , Mycobacterium tuberculosis and Caenorhabditis elegans , with Swiss Prot accession numbers P22033, P11653, P16332, P27253, P71774.1 and Q23381, respectively. Open and close boxes represent helices and 3(10) helices, respectively, and the arrow refers to the Asn-55 residue which is conserved in humans...”
- More
MUTA_MOUSE / P16332 Methylmalonyl-CoA mutase, mitochondrial; MCM; Methylmalonyl-CoA isomerase; EC 5.4.99.2 from Mus musculus (Mouse) (see paper)
NP_032676 methylmalonyl-CoA mutase, mitochondrial precursor from Mus musculus
66% identity, 94% coverage
- function: Catalyzes the reversible isomerization of methylmalonyl-CoA (MMCoA) (generated from branched-chain amino acid metabolism and degradation of dietary odd chain fatty acids and cholesterol) to succinyl-CoA (3-carboxypropionyl-CoA), a key intermediate of the tricarboxylic acid cycle.
catalytic activity: (R)-methylmalonyl-CoA = succinyl-CoA (RHEA:22888)
cofactor: adenosylcob(III)alamin
subunit: Homodimer. Interacts (the apoenzyme form) with MMAA; the interaction is GTP dependent. - Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency.
Forny, Nature metabolism 2023 - GeneRIF: Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency.
- Promoterless, Nuclease-Free Genome Editing Confers a Growth Advantage for Corrected Hepatocytes in Mice With Methylmalonic Acidemia.
Chandler, Hepatology (Baltimore, Md.) 2021 - GeneRIF: Promoterless, Nuclease-Free Genome Editing Confers a Growth Advantage for Corrected Hepatocytes in Mice With Methylmalonic Acidemia.
- New in vitro model derived from brain-specific Mut-/- mice confirms cerebral ammonium accumulation in methylmalonic aciduria.
Remacle, Molecular genetics and metabolism 2018 (PubMed)- GeneRIF: We confirmed significant NH4(+) accumulation in culture media of Mut(-/-) aggregates, suggesting that intracellular NH4(+) concentrations might even be higher, gave first clues on the mechanisms leading to NH4(+) accumulation in Mut(-/-) brain cells, and showed the involvement of neuroinflammatory processes in the neuropathophysiology of Methylmalonic aciduria .
- Novel Mouse Models of Methylmalonic Aciduria Recapitulate Phenotypic Traits with a Genetic Dosage Effect.
Forny, The Journal of biological chemistry 2016 - GeneRIF: On a high protein diet, mutant mice display disease exacerbation, including elevated blood ammonia, and catastrophic weight loss, which, in Mut(ki/ki) mice, is rescued by hydroxocobalamin treatment. This study expands knowledge of MMAuria, introduces the discovery of new biomarkers, and constitutes the first in vivo proof of principle of cobalamin treatment in mut-type MMAuria.
- The methylmalonic aciduria related genes, Mmaa, Mmab, and Mut, are broadly expressed in placental and embryonic tissues during mouse organogenesis.
Moreno-Garcia, Molecular genetics and metabolism 2012 (PubMed)- GeneRIF: The mouse methylmalonic aciduria- related genes, Mmaa, Mmab, and Mut may have specialized functions depending on the tissue or cell type.
- Mitochondrial dysfunction in mut methylmalonic acidemia.
Chandler, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2009 - GeneRIF: Mitochondrial dysfunction in Mut is reported.
- Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans.
Calvo, Proceedings of the National Academy of Sciences of the United States of America 2009 - GeneRIF: Includes the study of an upstream ORF in this gene, and shows that it functions to reduce protein levels by ~61%.
- A knock-out mouse model for methylmalonic aciduria resulting in neonatal lethality.
Peters, The Journal of biological chemistry 2003 (PubMed)- GeneRIF: methylmalonyl-CoA mutase has a role in methylmalonic aciduria and early neonatal lethality
- VPS13D affects epileptic seizures by regulating mitochondrial fission and autophagy in epileptic rats.
Wang, Genes & diseases 2024 - “...Table 1 Group Protein accession (UniProt accession) Up-regulated O08553 O35345 O70251 P08003 P09528 P10404 P11440 P16332 P17918 P23116 P24452 P27612 P31938 P32233 P38647 P43883 P47226 P48678 P52293 P59325 P62196 P70362 Q03145 Q5XJY5 Q61599 Q61838 Q62351 Q64133 Q64337 Q6P1B1 Q6P2B1 Q80X90 Q8BJ71 Q8BMA6 Q91VI7 Q922R8 Q99KK7 Q99LX0...”
- ISG15 Is a Novel Regulator of Lipid Metabolism during Vaccinia Virus Infection.
Albert, Microbiology spectrum 2022 - “...1 3.38 P32020 Scp2 Sterol carrier protein 2 3.24 Q9D1I5 Mcee Methylmalonyl-CoA epimerase, mitochondrial 3.02 P16332 Mmut Methylmalonyl-CoA mutase, mitochondrial 6.67 Q8CAY6 Acat2 Acetyl-CoA acetyltransferase, cytosolic 8.05 Lipid synthesis Q9D517 Agpat3 1-Acyl- sn -glycerol-3-phosphate acyltransferase gamma 4.87 Q8BYI6 Lpcat2 Lysophosphatidylcholine acyltransferase 2 2.88 Q8CHK3 Mboat7 Lysophospholipid...”
- 2D DIGE proteomic analysis reveals fasting-induced protein remodeling through organ-specific transcription factor(s) in mice
Kamata, FEBS open bio 2018 - “...mitochondrial Q8VCW8 Acsf2 Mm.386885 134 49% 25/96 68591 8.44 69 1.18 0.011 MethylmalonylCoA mutase, mitochondrial P16332 Mut Mm.259884 79 36% 19/64 83248 6.45 70 1.18 0.009 Glutathione S transferase 1 P10649 Gstm1 Mm.37199 169 77% 21/49 26067 7.71 71 1.14 0.027 Glyceraldehyde3phosphate dehydrogenase P16858 Gapdh Mm.304088...”
- Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
Ayyar, Journal of proteomics 2017 - “...L-malate from fumarate UP/DOWN O88989 Mdh1 Malate dehydrogenase Reversible oxidation of malate to oxaloacetate UP P16332 Mut Methylmalonyl-CoA mutase, mitochondrial Degradation of amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA UP Q920L2 Sdha Succinate dehydrogenase, mitochondrial Electron transfer from succinate to ubiquinone (coenzyme Q) UP/DOWN...”
- Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants
Ghoraba, Meta gene 2015 - “...coli , Mycobacterium tuberculosis and Caenorhabditis elegans , with Swiss Prot accession numbers P22033, P11653, P16332, P27253, P71774.1 and Q23381, respectively. Open and close boxes represent helices and 3(10) helices, respectively, and the arrow refers to the Asn-55 residue which is conserved in humans and in...”
- CypD(-/-) hearts have altered levels of proteins involved in Krebs cycle, branch chain amino acid degradation and pyruvate metabolism
Menazza, Journal of molecular and cellular cardiology 2013 - “...60 kDa heat shock protein, mitochondrial CH60_MOUSE 54.10 326 0.997 0.025 1.139 0.053 0.052 14 (P16332) Methylmalonyl-CoA mutase, mitochondrial MUTA_MOUSE 10.56 6 0.932 0.027 1.055 0.026 0.017 13 (P35486) Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial ODPA_MOUSE 50.77 55 1.060 0.029 1.178 0.013 0.009...”
ING2E5A_1517 methylmalonyl-CoA mutase from Petrimonas mucosa
69% identity, 93% coverage
- The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
Maus, Microorganisms 2020 - “...ING2E5A_1054 1.2.4.2, 2.3.1.61 Oxoglutarate dehydrogenase (succinyl-transferring), Dihydrolipoyllysine-residue succinyltransferase 2-oxoglutarate succinyl-CoA suc A, suc B ING2E5A_1515, ING2E5A_1517 5.4.99.2 Methylmalonyl-CoA mutase ( R )-methylmalonyl-CoA <=> succinyl-CoA mut A, mut B ING2E5A_1046 5.1.99.1 Methylmalonyl-CoA epimerase ( R )-methylmalonyl-CoA <=> ( S )-2-Methylmalonyl-CoA ING2E5A_1045, ING2E5A_1864 6.4.1.3 Propionyl-CoA carboxylase ATP +...”
EG14_03150, PGTDC60_0641 methylmalonyl-CoA mutase from Porphyromonas gingivalis
PGN_0456 methylmalonyl-CoA mutase large subunit from Porphyromonas gingivalis ATCC 33277
68% identity, 94% coverage
Caur_2508 / A9WI23 methylmalonyl-CoA mutase large subunit (EC 5.4.99.2) from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (see paper)
Caur_2508 methylmalonyl-CoA mutase, large subunit from Chloroflexus aurantiacus J-10-fl
66% identity, 97% coverage
- Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Tang, BMC genomics 2011 - “...(Caur_1648), accB (Caur_3739), mcr (Caur_2614), pcs (Caur_ 0613), pccB (Caur_2034, Caur_3435), mcee (Caur_3037), mut (Caur_1844, Caur_2508, Caur_2509), smtA (Caur_0179), smtB (Caur_0178), sdhBAC (Caur_1880 to Caur_1882), fh (Caur_1443), mcl (Caur_0174), mch (Caur_0173), mct (Caur_0174), meh (Caur_0180) Glycolate assimilation and glyoxylate cycle glcDEF (Caur_1144 - 1145, Caur_2133, Caur_2135),...”
- “...methylmalonyl-CoA epimerase ( mcee , Caur_3037), (6) L -methylmalonyl-CoA mutase (MCM) ( mut , Caur_1844, Caur_2508, Caur_2509), (7) succinyl-CoA:( S )-malyl-CoA transferase ( smtA (Caur_0179), smtB (Caur_0178)), (8) succinate dehydrogenase ( sdhBAC , Caur_1880 to Caur_1882), (9) fumarate hydratase ( fh , Caur_1443), (10) ( S...”
BAB1_1212 Methylmalonyl-CoA mutase, N-terminal:Methylmalonyl-CoA mutase:Coenzyme B12-binding:Methylmalonyl-CoA mutase, C-terminal from Brucella melitensis biovar Abortus 2308
67% identity, 95% coverage
BT2090, BT_2090 methylmalonyl-CoA mutase large subunit from Bacteroides thetaiotaomicron VPI-5482
WP_008759796 methylmalonyl-CoA mutase from Bacteroides thetaiotaomicron VPI-5482
66% identity, 97% coverage
- Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins
Putnam, mBio 2022 - “...BT_0343), HpnR / Hyp (B 12 -binding domain/radical SAM domain protein; BT_0640), MutAB (methylmalonyl-CoA mutase; BT_2090 and BT_2091), and NrdJ (B 12 -dependent ribonucleotide reductase; BT_2145) ( 12 , 16 , 25 27 ). Of these, four (MetH, HpnR/Hyp, NrdJ, and MutAB) bound to B 12...”
- Bacteroides methylmalonyl-CoA mutase produces propionate that promotes intestinal goblet cell differentiation and homeostasis.
Wang, Cell host & microbe 2024 (PubMed)- GeneRIF: Bacteroides methylmalonyl-CoA mutase produces propionate that promotes intestinal goblet cell differentiation and homeostasis.
BMEI0799 METHYLMALONYL-COA MUTASE from Brucella melitensis 16M
67% identity, 93% coverage
- Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis
Khan, Bioengineering (Basel, Switzerland) 2022 - “...aconitate hydratase (BMEI1855), (BMEII0009), (BMEI1952), (BMEII1061), (BMEI1939), (BMEII1060), (BMEII1062), (BMEII1064); and ureidoglycolate lyase (allA) and (BMEI0799). The PPI results showed that isocitrate lyase had a total number of nodes 11, average node numbers 7.09, average local clustering coefficient 0.95, the total number of edges 39, PPI...”
F1KWB3 methylmalonyl-CoA mutase from Ascaris suum
64% identity, 94% coverage
Q8MI68 methylmalonyl-CoA mutase (EC 5.4.99.2) from Sus scrofa (see paper)
NP_999570 methylmalonyl-CoA mutase, mitochondrial precursor from Sus scrofa
65% identity, 93% coverage
- Bioinformatics-based Characterization of the Sequence Variability of Zika Virus Polyprotein and Envelope Protein (E).
Polanco, Evolutionary bioinformatics online 2022 - “...CAM-E Q9S850, Q9X3Y6, and GW. Q32-E SVTP, and GW. POL-P E9L7A5, A0A142I5B9, P24230, POL-P, Q9MA50, Q8MI68, A8MLD3, B6HJU4, P0C988, P50569, Q5QMN5, Q9MYY0, Q0CBN5, Q7VPJ7, A5EXM7, Q5BJH7, Q7UH14, Q0BV25, P0C987, Q65215, Q8XD86, Q9GKL2, Q13B10, Q9ZBD8, E9D269, Q8ZRP8, P53678, P97784, P53677, P75464, Q32Q86, Q96PY5, C3LN54, Q9KRB0, P29365, Q29003,...”
- Influence of methylmalonyl-CoA mutase alleles on resistance to bovine tuberculosis in the European wild boar (Sus scrofa).
Naranjo, Animal genetics 2008 (PubMed)- GeneRIF: MUTm-B allele was associated with disease in a dominant pattern, while the MUTm AA genotype appeared to have a protective effect against bTB infection
Q23381 methylmalonyl-CoA mutase (EC 5.4.99.2) from Caenorhabditis elegans (see paper)
65% identity, 94% coverage
PFJ30894_RS04260 methylmalonyl-CoA mutase from Phascolarctobacterium faecium
65% identity, 96% coverage
F1KUP0 methylmalonyl-CoA mutase subunit (EC 5.4.99.2) from Ascaris suum (see paper)
64% identity, 94% coverage
Amuc_1983 methylmalonyl-CoA mutase from Akkermansia muciniphila ATCC BAA-835
66% identity, 96% coverage
WP_031931429 methylmalonyl-CoA mutase from Akkermansia muciniphila
66% identity, 96% coverage
mutB / AAA03041.1 methylmalonyl-CoA large subunit from Streptomyces cinnamonensis (see paper)
65% identity, 95% coverage
AMED_0914 methylmalonyl-CoA mutase from Amycolatopsis mediterranei U32
64% identity, 98% coverage
8gjuJ / P22033 Crystal structure of human methylmalonyl-coa mutase (mmut) in complex with methylmalonic acidemia type a protein (mmaa), coenzyme a, and gdp (see paper)
65% identity, 97% coverage
- Ligand: coenzyme a (8gjuJ)
WP_004694550 methylmalonyl-CoA mutase from Veillonella sp.
64% identity, 96% coverage
mcm / CAJ91090.1 methylmalonyl-CoA mutase from Sorangium cellulosum (see paper)
65% identity, 76% coverage
Q2RRG6 methylmalonyl-CoA mutase from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
Rru_A2479 Methylmalonyl-CoA mutase-like from Rhodospirillum rubrum ATCC 11170
65% identity, 95% coverage
MCM_RHIME / O86028 Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 from Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti) (see 2 papers)
SMb20757 methylmalonyl-CoA mutase protein from Sinorhizobium meliloti 1021
64% identity, 98% coverage
- function: Radical enzyme that catalyzes the transformation of methylmalonyl-CoA to succinyl-CoA. Is required for growth on the polyhydroxyalkanoate degradation pathway intermediates 3- hydroxybutyrate and acetoacetate as sole carbon source.
catalytic activity: (R)-methylmalonyl-CoA = succinyl-CoA (RHEA:22888)
cofactor: adenosylcob(III)alamin
cofactor: a monovalent cation (Monovalent cations such as NH4(+), Rb(+), Cs(+), K(+), Li(+) or Na(+) are required for enzyme activity.)
subunit: Homodimer.
disruption phenotype: Cells lacking this gene show no methylmalonyl-CoA mutase activity, in contrast to wild-type. - Role of the regulatory gene rirA in the transcriptional response of Sinorhizobium meliloti to iron limitation
Chao, Applied and environmental microbiology 2005 - “...SMb20099 SMb20127 SMb20203 SMb20545 SMb20600 SMb20755 SMb20757 SMb20924 SMb20946 SMb20949 SMb20959 SMb20960 SMb20993 SMb21285 SMb21337 SMb21432 SMb21456...”
RLV_2267 methylmalonyl-CoA mutase from Rhizobium leguminosarum bv. viciae
64% identity, 98% coverage
SACE_5639 methylmalonyl-CoA mutase from Saccharopolyspora erythraea NRRL 2338
63% identity, 90% coverage
- Reconstruction of the Genome-Scale Metabolic Model of Saccharopolyspora erythraea and Its Application in the Overproduction of Erythromycin
Xu, Metabolites 2022 - “...Four metabolic targets acquired from previous reports: SACE_0728 [ 2 ], SACE_0731 [ 17 ], SACE_5639 [ 5 , 18 ], and SACE_6669 [ 19 ], were used to simulate the single-gene knockout experiment. The comparison in Table S1 revealed that the simulations for the four...”
- Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Wu, Journal of biological engineering 2019 - “...subunit, SACE_1171 ; malate dehydrogenase, SACE_3674 ; methylmalonyl-CoA mutase subunit beta, SACE_5638 ; methylmalonyl-CoA mutase, SACE_5639 ; succinyl-CoA synthetase subunit alpha, SACE_6668 ; succinyl-CoA synthetase subunit beta, SACE_6669 ; phosphoenolpyruvate carboxykinase, SACE_7274 ) were analyzed by qRT-PCR. Compared to A226, SACE_1171 was transcriptionally down-regulated by 2.4-...”
- Blocking the flow of propionate into TCA cycle through a mutB knockout leads to a significant increase of erythromycin production by an industrial strain of Saccharopolyspora erythraea
Chen, Bioprocess and biosystems engineering 2017 (PubMed)- “...erythraea HL3168 E3-DmutB was constructed by deleting mutB (SACE_5639) gene encoding the beta subunit of methylmalonyl-CoA mutase of an industrial strain of S....”
- “...direction of methylmalonylCoA through the knockout of the mutB (SACE_5639) gene was a good strategy for improving the Er-A yield in wildtype strains in a...”
- Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea
Karničar, Microbial cell factories 2016 - “...number of genes of the TCA cycle and fatty acid metabolism, as well as mutB (SACE_5639, a member of the mcm operon involved in converting between succinyl- and methylmalonyl-CoA). These genes are expected to be involved in the supply of precursors for erythromycin biosynthesis from the...”
MAB_2711c Probable methylmalonyl-CoA mutase large subunit MutB from Mycobacterium abscessus ATCC 19977
62% identity, 92% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M. xenopi M.szulgai M. smegmatis Accession number GCA_000157895.1 GCA_002705835 GCA_001582015...”
- “...B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase MAB_2129 605.9966667 39.45958101 MSMEG_0093 94.66 39.15167557 mutB Methylmalonyl-CoA mutase MAB_2711c 180.9466667 2.206928484 nrdZ Ribonucleotide reductase of class II Gene name Description M. tuberculosis Locus Rich 7H9 broth Cholesterol Macrophages Average SD Average SD Average SD All genes 256.0163876 551.1120531 256.01...”
Q84FZ1 methylmalonyl-CoA mutase (EC 5.4.99.2) from Methylorubrum extorquens (see paper)
66% identity, 95% coverage
MSMEG_3159 methylmalonyl-CoA mutase large subunit from Mycobacterium smegmatis str. MC2 155
MSMEG_3159 methylmalonyl-CoA mutase from Mycolicibacterium smegmatis MC2 155
62% identity, 93% coverage
CCNA_02459 methylmalonyl-CoA mutase alpha subunit from Caulobacter crescentus NA1000
63% identity, 98% coverage
PFCIRM129_07240, PFREUD_07650 methylmalonyl-CoA mutase from Propionibacterium freudenreichii subsp. freudenreichii
63% identity, 94% coverage
mutB / P11653 methylmalonyl-CoA mutase large subunit (EC 5.4.99.2) from Propionibacterium freudenreichii subsp. shermanii (see 8 papers)
MUTB_PROFR / P11653 Methylmalonyl-CoA mutase large subunit; MCM-alpha; EC 5.4.99.2 from Propionibacterium freudenreichii subsp. shermanii (see 4 papers)
P11653 methylmalonyl-CoA mutase (EC 5.4.99.2) from Propionibacterium freudenreichii subsp. shermanii (see paper)
63% identity, 94% coverage
- function: Catalyzes the reversible conversion of succinyl-CoA to (R)- methylmalonyl-CoA through a radical mechanism (PubMed:9772164). Is involved in the fermentation of pyruvate to propanoate that occurs in Propionibacteria (Probable).
catalytic activity: (R)-methylmalonyl-CoA = succinyl-CoA (RHEA:22888)
cofactor: adenosylcob(III)alamin
subunit: Heterodimer of an alpha and a beta chain. - How haptophytes microalgae mitigate vitamin B12 limitation
Nef, Scientific reports 2019 - “...norvegicus CBLA (D3ZNY3), Homo sapiens CBLB (Q96EY8) and MMCM (P22033), Propionibacterium freudenreichii subsp. shermanii MMCM (P11653). Homologous genes identified this way were searched again in T . lutea genome using TBlastX (expected threshold 1E-1). Conserved functional domains were identified by alignment of nucleic and proteic sequences...”
- Order in Disorder as Observed by the "Hydrophobic Cluster Analysis" of Protein Sequences.
Bitard-Feildel, Proteomics 2018 (no snippet) - Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants
Ghoraba, Meta gene 2015 - “...Escherichia coli , Mycobacterium tuberculosis and Caenorhabditis elegans , with Swiss Prot accession numbers P22033, P11653, P16332, P27253, P71774.1 and Q23381, respectively. Open and close boxes represent helices and 3(10) helices, respectively, and the arrow refers to the Asn-55 residue which is conserved in humans and...”
- Novel B(12)-dependent acyl-CoA mutases and their biotechnological potential
Cracan, Biochemistry 2012 - “...shown on the right. The following proteins were used as examples: MCMs ( Propionibacterium shermanii ()(P11653, P11652), E. coli (2)(AAA69084), Metallosphaera sedula (22)(Msed_0638, Msed_2055) and Bacillus tusciae (22)(YP_003589181)); ICM ( Streptomyces cinnamonensis (22)(AAC08713, CAB59633)), IcmF ( Geobacillus kaustophilus (2)(YP_149244)), HCM ( Rhodobacter sphaeroides (22)(Rsph17029_3657, Rsph17029_3654)), and...”
- Gene cluster involved in the biosynthesis of griseobactin, a catechol-peptide siderophore of Streptomyces sp. ATCC 700974
Patzer, Journal of bacteriology 2010 - “...MutB (728; C-terminal 347 amino acids)/ Propionibacterium freudenreichii (P11653) 68, 79 43, 58 54, 74 halves that display 29% sequence identity to each other....”
- Diverse protein regulations on PHA formation in Ralstonia eutropha on short chain organic acids
Lee, International journal of biological sciences 2009 - “...(21) P42415 Bacillus subtilis Acetyl-CoA biosynthesis (propionyl-CoA metabolism) Methylmalonyl-CoA mutase large subunit 6 42 (25) P11653 Propionibacterium freudenreichii shermanii Propionic acid fermentation Carnitine O-acetyltransferase 2 30 (29) G90608 Mycoplasma pulmonis -oxidation pathway Probable acyl-CoA dehydrogenase FadE22b 3 43 (26) Q7TXC4_MYCBO Mycobacterium bovis -oxidation pathway 3-oxoacyl-acyl-carrier protein...”
Ga0102493_112759 methylmalonyl-CoA mutase from Erythrobacter litoralis
63% identity, 96% coverage
- Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light
Fiebig, Molecular microbiology 2019 - “...transcript provided efficient amplification in one-step qRT-PCR reactions (see Materials and Methods ). Gene locus Ga0102493_112759, which encodes a methylmalonyl-CoA mutase, was selected as a control gene for normalization ( Figure S3 ). In our RNA-seq data sets, transcripts for this gene were abundant (in the...”
- “...database under accession GSE126532. qRT-PCR The GSR-dependent transcript, dps (Ga0102493_111653), and an endogenous control transcript (Ga0102493_112759) were evaluated using TaqMan probes and SuperScript III Platinum One-Step qRT-PCR Kit (Invitrogen) with a QuantStudio 5 real time PCR system (Thermo Fisher). The primer-probe sets ( dps F TCTCATCGCCGAACTCAAC;...”
6oxdA / P9WJK5 Structure of mycobacterium tuberculosis methylmalonyl-coa mutase with adenosyl cobalamin (see paper)
63% identity, 93% coverage
- Ligands: cobalamin; itaconyl coenzyme a (6oxdA)
1e1cA / P11653 Methylmalonyl-coa mutase h244a mutant (see paper)
63% identity, 94% coverage
- Ligands: cobalamin; desulfo-coenzyme a (1e1cA)
Mb1530 PROBABLE METHYLMALONYL-COA MUTASE LARGE SUBUNIT MUTB (MCM) from Mycobacterium bovis AF2122/97
Rv1493 methylmalonyl-CoA mutase from Mycobacterium tuberculosis H37Rv
62% identity, 92% coverage
- Differential gene expression between Mycobacterium bovis and Mycobacterium tuberculosis
Rehren, Tuberculosis (Edinburgh, Scotland) 2007 - “...Mb1456 3.6 0.00523 Conserved hypothetical protein Rv1493 Mb1530 mutB 3.1 0.0224 Probable methylmalonyl-coa mutase Rv1588c Mb1614c 3.3 0.0164 Partial REP13E12...”
- Comparative Genomic Analysis of Mycobacterium tuberculosis Isolates Circulating in North Santander, Colombia
Bohada-Lizarazo, Tropical medicine and infectious disease 2024 - “...SigI CDS SNP Transversion 5.60% 21088X7 Truncation rv1329c DinG CDS SNP Transversion 5.60% 21088X10 Truncation rv1493 MutB CDS SNP Transition 47.10% 21088X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13, X15, X16, X17, X18 Truncation rv1494 MazE4 CDS SNP Transversion 47.10% 21088X2, X3,...”
- Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex
Brenner, BMC medical genomics 2023 - “...2100 161 1 Rv1491c Conserved membrane protein Synonymous 1,684,979 0 0.948 4100 2080 172 1 Rv1493 MutB Probable methylmalonyl-CoA mutase large subunit MutB (MCM) Synonymous 1,739,294 0 0.998 4100 2250 9 3 Rv1536 IleS Isoleucyl-tRNA synthetase IleS In vitro essential per multiple studies (Minato 2019; DeJesus...”
- “...FadE5 Required for growth on cholesterol (Griffin 2011) 1,684,979 0 0.948 4100 2080 172 1 Rv1493 MutB Synonymous Probable methylmalonyl-CoA mutase large subunit MutB (MCM) Downstream in cholesterol to propionyl-CoA metabolic pathways (Wilburn 2018) 1,754,572 0 0.951 4100 2100 161 1 Rv1550 FadD11 Leu286Ser Probable fatty-acid-CoA...”
- Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
Sanoussi, Microbial genomics 2021 - “...of the 30 genes is an essential gene (Mycobrowser). The 30 genes formed 2 regions: Rv1493 through Rv1509 (L5.3.2-Del region 1) and Rv1511 through Rv1521 (L5.3.2-Del region 2), separated by the gene Rv1510 , which is present in the L5.3.2 isolate. All genes in the table...”
- “...% ( n =202) Rv1492 # ( mutA ) 1848bp 16821571684004 Lipid metabolism 100 (202) Rv1493 (mutB) 2253bp 16840051686257 Lipid metabolism 97 (196) Rv1494 (mazE4) 303bp 16862711686573 Virulence, detoxification, adaptation 97 (196) Rv1495 (mazF4) 318bp 16865701686887 Virulence, detoxification, adaptation 97 (196) Rv1496 1005bp 16868841687888 Cell wall...”
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M. xenopi M.szulgai M. smegmatis Accession number GCA_000157895.1 GCA_002705835...”
- “...dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c 155.78 9.823003614 311.4966667 16.31473431 128.15 45.50090622 mutB Methylmalonyl-CoA mutase Rv1493 48.83 1.851323851 139.7433333 70.5155852 38.08333333 53.8579665 nrdZ Ribonucleotide reductase of class II Rv0570 60.79333333 1.360890232 366.2433333 120.7928051 119.6 101.265619 Studies with Propionibacterium sp. showed the crucial role of cobA gene...”
- Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains
Ullah, Pathogens (Basel, Switzerland) 2021 - “...chain RibH (6,7-dimethyl-8-ribityllumazine synthase) (DMRL synthase) (lumazine synthase) intermediary metabolism and respiration RR and XDR Rv1493 mutB Involved in propionic acid fermentation. Catalyzes the isomerization of succinyl-CoA to methylmalonyl-CoA during synthesis of propionate from tricarboxylic acid-cycle intermediates [catalytic activity: ( R )-2-methyl-3-oxopropanoyl-CoA = succinyl-CoA] Probable methylmalonyl-CoA...”
- Propionate metabolism in a human pathogenic fungus: proteomic and biochemical analyses
Santos, IMA fungus 2020 - “...sequences of methylmalonyl-CoA mutases from C. elegans (accession number CAA84676) and M. tuberculosis (Rv1492 and Rv1493) (Savvi et al. 2008 ) shows no homologue in Paracoccidioides spp. Thus, it is unlikely that these fungi employ the methylmalonyl-CoA pathway in degradation of propionyl-CoA as previously shown for...”
- Establishment of a Host-to-Host Transmission Model for Mycobacterium avium subsp. hominissuis Using Caenorhabditis elegans and Identification of Colonization-Associated Genes
Bermudez, Frontiers in cellular and infection microbiology 2018 - “...93.8 MAVA5_03280 Mycothiol acetyltransferase MAV_0761, Rv0819, MAB_0748/112 n N-terminus H8 93.7 MAVA5_14105 Methylmalonyl-CoA mutase MAV_3277, Rv1493, MAB_2711c/110 n N-terminus H4 92.2 MAVA5_09730 Hydrolase MAV_2243, Rv2223c, MAB_1919/106 n N-terminus E6 91.5 MAVA5_15805 Acyl-CoA dehydrogenase MAV_3616, Rv2724c, MAB_3040c/120 n N-terminus G5 90.1 MAVA5_18755 Serine/threonine protein kinase MAV_4238, Rv0931c/96...”
- More than cholesterol catabolism: regulatory vulnerabilities in Mycobacterium tuberculosis
Bonds, Current opinion in chemical biology 2018 - “...TCA Cycle & Glyoxylate Cycle Malate dehydrogenase Rv1492 MutA Methylmalonyl-CoA Pathway Methylmalonyl-CoA mutase (small subunit) Rv1493 MutB Methylmalonyl-CoA Pathway Methylmalonyl-CoA mutase (large subunit) Rv1837c GlcB Glyoxylate Cycle Malate synthase G Rv2215 DlaT Pyruvate Transformation Pyruvate dehydrogenase E2 component Rv2241 AceE Pyruvate Transformation Pyruvate dehydrogenase E1 component...”
- More
YliK / b2917 methylmalonyl-CoA mutase (EC 5.4.99.2) from Escherichia coli K-12 substr. MG1655 (see 5 papers)
scpA / P27253 methylmalonyl-CoA mutase (EC 5.4.99.2) from Escherichia coli (strain K12) (see 4 papers)
SCPA_ECOLI / P27253 Methylmalonyl-CoA mutase; MCM; EC 5.4.99.2 from Escherichia coli (strain K12) (see 3 papers)
A0A140N835 methylmalonyl-CoA mutase from Escherichia coli (strain B / BL21-DE3)
NP_417392 methylmalonyl-CoA mutase from Escherichia coli str. K-12 substr. MG1655
b2917 methylmalonyl-CoA mutase from Escherichia coli str. K-12 substr. MG1655
61% identity, 98% coverage
- function: Catalyzes the interconversion of succinyl-CoA and methylmalonyl-CoA. Could be part of a pathway that converts succinate to propionate.
catalytic activity: (R)-methylmalonyl-CoA = succinyl-CoA (RHEA:22888)
cofactor: adenosylcob(III)alamin
subunit: Homodimer. Interacts with ArgK. - Efficient overexpression and purification of severe acute respiratory syndrome coronavirus 2 nucleocapsid proteins in Escherichia coli
Brudenell, The Biochemical journal 2024 - “...LacI (A0A140NB96) which is encoded on the expression plasmid used in our work, methylmalonyl-CoA mutase (A0A140N835), sulfate ABC transporter (A0A140N7X7) and another transcriptional regulator, IclR (A0A140NF03). All contaminants over 0.1% are shown in Supplementary Figure S6 . Response of Ncap variants with pooled antisera We have...”
- Sleeping beauty mutase (sbm) is expressed and interacts with ygfd in Escherichia coli.
Froese, Microbiological research 2009 - GeneRIF: Sbm is expressed and interacts with ygfD in Escherichia coli.
- Functional Prediction of Biological Profile During Eutrophication in Marine Environment
Sbaoui, Bioinformatics and biology insights 2022 - “...sigma 54 (sigma N) factor RseP P0AEH1 Intramembrane zinc metalloprotease RtxA A0A3L0W7I6 Multifunctional-autoprocessing repeats-in-toxin ScpA P27253 Methylmalonyl-coa epimerase SdhA P0AC41 Succinate dehydrogenase SdhA P0AC41 Succinate: quinone oxidoreductase, FAD binding protein SeqA P0AFY8 Negative modulator of initiation of replication SoxR P0ACS2 DNA-binding transcriptional dual regulator Sqr P0AC41...”
- Mutation analysis of methylmalonyl CoA mutase gene exon 2 in Egyptian families: Identification of 25 novel allelic variants
Ghoraba, Meta gene 2015 - “..., Mycobacterium tuberculosis and Caenorhabditis elegans , with Swiss Prot accession numbers P22033, P11653, P16332, P27253, P71774.1 and Q23381, respectively. Open and close boxes represent helices and 3(10) helices, respectively, and the arrow refers to the Asn-55 residue which is conserved in humans and in mice....”
- Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme
Sokolovskaya, mBio 2019 - “...the theoretical extinction coefficient 55,810 M 1 cm 1 ( 125 ). Ec MCM (locus b2917, scpA , previously sbmA ) was expressed with an N-terminal 6His tag from a pET28a vector in E. coli BL21(DE3), by induction at an OD 600 of 0.6 to 0.8...”
CRM90_15015 methylmalonyl-CoA mutase from Mycobacterium sp. ENV421
62% identity, 91% coverage
MAV_3277 methylmalonyl-CoA mutase large subunit from Mycobacterium avium 104
MAVA5_14105 methylmalonyl-CoA mutase from Mycobacterium avium subsp. hominissuis A5
62% identity, 92% coverage
- Establishment of a Host-to-Host Transmission Model for Mycobacterium avium subsp. hominissuis Using Caenorhabditis elegans and Identification of Colonization-Associated Genes
Bermudez, Frontiers in cellular and infection microbiology 2018 - “...D3 93.8 MAVA5_03280 Mycothiol acetyltransferase MAV_0761, Rv0819, MAB_0748/112 n N-terminus H8 93.7 MAVA5_14105 Methylmalonyl-CoA mutase MAV_3277, Rv1493, MAB_2711c/110 n N-terminus H4 92.2 MAVA5_09730 Hydrolase MAV_2243, Rv2223c, MAB_1919/106 n N-terminus E6 91.5 MAVA5_15805 Acyl-CoA dehydrogenase MAV_3616, Rv2724c, MAB_3040c/120 n N-terminus G5 90.1 MAVA5_18755 Serine/threonine protein kinase MAV_4238,...”
- Establishment of a Host-to-Host Transmission Model for Mycobacterium avium subsp. hominissuis Using Caenorhabditis elegans and Identification of Colonization-Associated Genes
Bermudez, Frontiers in cellular and infection microbiology 2018 - “...104 n N-terminus D3 93.8 MAVA5_03280 Mycothiol acetyltransferase MAV_0761, Rv0819, MAB_0748/112 n N-terminus H8 93.7 MAVA5_14105 Methylmalonyl-CoA mutase MAV_3277, Rv1493, MAB_2711c/110 n N-terminus H4 92.2 MAVA5_09730 Hydrolase MAV_2243, Rv2223c, MAB_1919/106 n N-terminus E6 91.5 MAVA5_15805 Acyl-CoA dehydrogenase MAV_3616, Rv2724c, MAB_3040c/120 n N-terminus G5 90.1 MAVA5_18755 Serine/threonine...”
WP_101348647 methylmalonyl-CoA mutase from Escherichia coli str. K-12 substr. MG1655
61% identity, 98% coverage
S3102 methylmalonyl-CoA mutase (MCM) from Shigella flexneri 2a str. 2457T
61% identity, 98% coverage
A4I2L1 methylmalonyl-CoA mutase from Leishmania infantum
63% identity, 96% coverage
MMAR_2303 methylmalonyl-CoA mutase large subunit, MutB from Mycobacterium marinum M
61% identity, 91% coverage
MCNS_22010 methylmalonyl-CoA mutase from Mycobacterium conspicuum
61% identity, 91% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M. xenopi M.szulgai M. smegmatis Accession number GCA_000157895.1 GCA_002705835 GCA_001582015 NZ_MBDY01000007.1...”
cg1725 methylmalonyl-CoA mutase from Corynebacterium glutamicum ATCC 13032
NCgl1471 methylmalonyl-CoA mutase from Corynebacterium glutamicum ATCC 13032
61% identity, 95% coverage
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...cg1551 cg1072 cg0475 cg2662 cg1575 cg1880 cg1290 cg2450 cg1725 cg2166 cg2323 cg2166 cg1629 cg0583 cg0482 cg2797 cg2958 cg0299 cg2429 cg1267 cg0655 cg1790 cg1790...”
- Formation and metabolism of methylmalonyl coenzyme A in Corynebacterium glutamicum
Botella, Journal of bacteriology 2009 - “...of the suborder Corynebacterineae and is encoded by NCgl1471, NCgl1472, and NCgl1470. In addition, we observe the presence of methylmalonate in C. glutamicum,...”
- “...in members of the suborder Corynebacterineae is discussed. (NCgl1471, NCgl1472), as well as a MeaB-encoding subunit (NCgl1470) overlapping the subunit by 4 bp,...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...NCgl0385 NCgl2340 NCgl1336 NCgl1607 NCgl1094 NCgl2150 NCgl1471 NCgl1900 NCgl2037 NCgl1900 NCgl1384 NCgl0478 NCgl0390 NCgl2451 NCgl2582 NCgl0242 NCgl2133...”
H16_A1949 Methylmalonyl-CoA mutase from Ralstonia eutropha H16
H16_A1949 methylmalonyl-CoA mutase from Cupriavidus necator H16
51% identity, 94% coverage
- Investigations on the microbial catabolism of the organic sulfur compounds TDP and DTDP in Ralstonia eutropha H16 employing DNA microarrays
Peplinski, Applied microbiology and biotechnology 2010 - “...dehydrogenase, short-chain specific 2.78 2.65 3.35 x H16_A0280 sbml Methylmalonyl-Coa mutase 9.72 6.11 4.05 x H16_A1949 sbm2 Methylmalonyl-Coa mutase 248.35 2.87 7.00 x H16_A2251 phaY1 d -()-3-hydroxybutyrate oligomer hydrolase 3.07 3.79 9.93 x H16_B1192 Acyl-CoA dehydrogenase 25.89 77.24 2.92 x D Genes putatively involved in the...”
- “...were detected, encoding a methylmalonyl-CoA mutase ( sbm1 , H16_A0280, four to tenfold; sbm2 , H16_A1949, 3- to 248-fold). This enzyme converts succinyl-CoA to methylmalonyl-CoA. Finally, genes for an ABC-type transporter of the NitT family (H16_A0357-A0359, 6- to 130-fold) exhibited increased expression levels at the first...”
DEFDS_1225 methylmalonyl-CoA mutase N-terminal domain from Deferribacter desulfuricans SSM1
52% identity, 75% coverage
O74009 methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) from Pyrococcus horikoshii (see paper)
PH1306 methylmalonyl-CoA mutase from Pyrococcus horikoshii OT3
53% identity, 72% coverage
WP_048053359 methylmalonyl-CoA mutase from Pyrococcus horikoshii OT3
53% identity, 72% coverage
TON_1110 methylmalonyl-CoA mutase, N-terminus of large subunit from Thermococcus onnurineus NA1
53% identity, 72% coverage
THA_155 methylmalonyl-CoA mutase, N- domain/subunit from Thermosipho africanus TCF52B
52% identity, 72% coverage
SCO6832 methylmalonyll-CoA mutase from Streptomyces coelicolor A3(2)
51% identity, 71% coverage
- Genome Analysis of a Variant of Streptomyces coelicolor M145 with High Lipid Content and Poor Ability to Synthetize Antibiotics
Dulermo, Microorganisms 2023 - “...of the deletions mentioned above. Furthermore, we noticed the deletion, in the TD variant, of sco6832 , one of the two genes encoding an L-methylmalonyl-CoA mutase. This enzyme catalyzes the conversion of L-methylmalonyl-CoA, originating from propionyl-CoA, into succinyl-CoA. We cannot exclude that the deletion of sco6832...”
- Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Lewis, BMC genomics 2010 - “...whose 5' terminus lies within a "region of difference" as "absent". For example, we classify SCO6832 (a methylmalonyl-CoA mutase) as being absent/divergent in S. lividans TK24. It is clear from the GACK classification of probe absences (see Additional Files 4 and 5 ) that SCO6832 is...”
- “...than three consecutive non binding probes, comprising the first probe within the gene, extends into SCO6832 from upstream so encompassing the translational start site of the gene within a 'region of difference', the gene is classified as absent/divergent according to the microarray data. However, the results...”
PTH_1361 methylmalonyl-CoA mutase N-terminal domain-containing protein from Pelotomaculum thermopropionicum SI
47% identity, 75% coverage
- Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T)
Visser, Standards in genomic sciences 2013 - “...mmcD2 Desku_1361 Succinyl-CoA synthetase, alpha subunit 78 PTH_1359 mmcE Desku_1362 Methylmalonyl-CoA mutase, N-terminal domain 77 PTH_1361 mmcF Desku_1363 Methylmalonyl-CoA mutase, C-terminal domain 82 PTH_1362 mmcG Desku_1364 Methylmalonyl-CoA epimerase 86 PTH_1363 mmcH Desku_1365 Methylmalonyl-CoA decarboxylase, alpha subunit 75 PTH_1364 mmcI Desku_1366 Methylmalonyl-CoA decarboxylase, epsilon subunit 82 PTH_1365...”
- Substrate-dependent transcriptomic shifts in Pelotomaculum thermopropionicum grown in syntrophic co-culture with Methanothermobacter thermautotrophicus
Kato, Microbial biotechnology 2009 - “...Nterminal domain ( mmcB , PTH_1356); open triangle, methylmalonylCoA mutase Nterminal domain ( mmcE , PTH_1361); filled square, predicted lactate dehydrogenase ( glcD , PTH_2230); asterisk, malic enzyme ( sfcA , PTH_2899). The approximation curve and correlation coefficient ( r ) are given. Overview of transcriptome...”
- “...mmcBR 5CGA TCT TGG TGT GGA TAA CT3; methylmalonylCoA mutase Nterminal domain ( mmcE , PTH_1361), mmcEF 5CAT CAG CGG CTA TCA TAT3 and mmcER 5TCA GGT GAG CAT TGA AGA3; predicted lactate dehydrogenase ( glcD , PTH_2230), ldhF 5GGG CTG GTT CTT TCC ACT C3...”
PFJ30894_RS04415 methylmalonyl-CoA mutase from Phascolarctobacterium faecium
48% identity, 72% coverage
AF1288a Methylmalonyl-CoA mutase, N-terminal domain/subunit from Archaeoglobus fulgidus DSM 4304
48% identity, 72% coverage
C9LNB3 Methylmalonyl-CoA mutase domain protein from Dialister invisus DSM 15470
GCWU000321_01033 methylmalonyl-CoA mutase from Dialister invisus DSM 15470
46% identity, 75% coverage
Sfum_0458 methylmalonyl-CoA mutase, large subunit from Syntrophobacter fumaroxidans MPOB
44% identity, 75% coverage
SY28_RS14080 methylmalonyl-CoA mutase from Meiothermus taiwanensis
49% identity, 70% coverage
Q39QL0 (R)-methylmalonyl-CoA mutase, isobutyryl-CoA mutase-like catalytic subunit from Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)
49% identity, 75% coverage
Q9HRZ1 Methylmalonyl-CoA mutase, subunit alpha from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
49% identity, 71% coverage
PFJ30894_RS03735 methylmalonyl-CoA mutase from Phascolarctobacterium faecium
47% identity, 71% coverage
CFX1CAM_1019 methylmalonyl-CoA mutase from Brevefilum fermentans
45% identity, 72% coverage
A4YEG1 methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) from Metallosphaera sedula (see paper)
Msed_0638 methylmalonyl-CoA mutase, large subunit from Metallosphaera sedula DSM 5348
WP_012020600 methylmalonyl-CoA mutase from Metallosphaera sedula DSM 5348
46% identity, 72% coverage
- Enzymes Catalyzing Crotonyl-CoA Conversion to Acetoacetyl-CoA During the Autotrophic CO2 Fixation in Metallosphaera sedula
Liu, Frontiers in microbiology 2020 - “...A. S. Adams M. W. Kelly R. M. ( 2012 ). Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert ( S )-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle. Appl. Environ. Microbiol. 78 6194 6202 . 10.1128/AEM.01312-12 22752162 Hawkins A. B. Adams M....”
- Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO2 fixation cycle in extremely thermoacidophilic archaea
Loder, Metabolic engineering 2016 - “...5 22064852 Han Y Hawkins AS Adams MW Kelly RM 2012 Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert ( S )-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle Appl Environ Microbiol 78 6194 202 22752162 Hansen T Urbanke C Leppanen VM Goldman...”
- “...S )-Methylmalonyl-CoA ( R )-Methylmalonyl-CoA R ( Marcheschi et al., 2012 ) Methylmalonyl-CoA mutase MCM Msed_0638 ( R )-Methylmalonyl-CoA Succinyl-CoA R ( Marcheschi et al., 2012 ) Msed_2055 Succinic semialdehyde reductase (NADPH) SSR Msed_1424 Succinic semialdehyde + NADPH 4-Hydroxybutyrate + NADP R ( Kockelkorn and Fuchs,...”
- Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota
Leyn, Journal of bacteriology 2015 - “...SSO2178 Msed_1993 Msed_1456 Msed_1426 Msed_0639 Msed_0638 Msed_2055 Msed_1424 Msed_1422 Msed_1321 Msed_0656 Msed_1423 Msed_0363- Msed_0364 Msed_0743 ST2485...”
- “...Kelly RM. 2012. Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera...”
- Conversion of 4-hydroxybutyrate to acetyl coenzyme A and its anapleurosis in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway
Hawkins, Applied and environmental microbiology 2014 - “...Msed_1375 Msed_0709 Msed_1993 Msed_1456 Msed_2001 Msed_1426 Msed_0639 Msed_0638, Msed_2055 Msed_1424 Msed_0406 Msed_1321 Msed_0399 Msed_0656 NCE (6, 34) R (35,...”
- “...Kelly RM. 2012. Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera...”
- Role of 4-hydroxybutyrate-CoA synthetase in the CO2 fixation cycle in thermoacidophilic archaea
Hawkins, The Journal of biological chemistry 2013 - “...Msed_0709 Msed_1993 Msed_1456 Msed_2001 Msed_1426 Msed_0639 Msed_0638 Msed_2055 Msed_1424 Msed_0394 Msed_0406 Msed_1321 Msed_0399 Msed_0656 CO2-H2 Autotrophy in...”
- “...Epimerase (Msed_ 0639) and mutase (Msed_0638, Msed_2055) convert (S)-methylmalonyl-CoA to succinyl-CoA in the Metallosphaera sedula...”
- Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle
Han, Applied and environmental microbiology 2012 - “...(Msed_0638 and Msed_2055) Convert (S)-Methylmalonyl-Coenzyme A (CoA) to Succinyl-CoA in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Cycle Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina,...”
- “...to that encoding the catalytic subunit of MCM- (Msed_0638), while the gene for the coenzyme B12-binding subunit of MCM (MCM-) is located remotely (Msed_2055)....”
- Novel B(12)-dependent acyl-CoA mutases and their biotechnological potential
Cracan, Biochemistry 2012 - “...8805541 16 Han Y Hawkins AS Adams MW Kelly RM Epimerase (Msed_ 0639) and Mutase (Msed_0638, Msed_2055) Convert (S)-Methylmalonyl-CoA to Succinyl-CoA in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Cycle App Environ Microbiol 2012 17 Menendez C Bauer Z Huber H Gad'on N Stetter KO Fuchs G Presence of...”
- Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota
Ramos-Vera, Journal of bacteriology 2011 - “...(e.g., small subunit Msed_2055 and large subunit Msed_0638). Interestingly, Msed_2056 (ArgK-like) overlaps with the ORF encoding the small MCM subunit...”
- Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle.
Han, Applied and environmental microbiology 2012 - GeneRIF: Methylmalonyl-CoA mutase and methylmalonyl-CoA epimerase together catalyzed the two-step conversion of (S)-methylmalonyl-CoA to succinyl-CoA, consistent with their proposed role in the 3-hydroxypropionate/4-hydroxybutyrate cycle.
HVO_1380 methylmalonyl-CoA mutase subunit A from Haloferax volcanii DS2
47% identity, 71% coverage
HVO_0893 methylmalonyl-CoA mutase subunit A from Haloferax volcanii DS2
42% identity, 71% coverage
SRIMR7_12355 methylmalonyl-CoA mutase from Streptomyces rimosus subsp. rimosus
43% identity, 72% coverage
XNRR2_1417 methylmalonyl-CoA mutase from Streptomyces albidoflavus
42% identity, 72% coverage
- Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2
Gläser, Microbial cell factories 2021 - “...genes of CoA metabolism revealed a more pronounced expression change. Isobutyryl-CoA mutase was strongly activated (XNRR2_1417, log 2 -fold 5.2), and the initial steps of the ethylmalonyl-CoA pathway, involving acetyl-CoA carboxylase (XNRR2_1438, XNRR2_1987) and acetyl-/propionyl-CoA carboxylase (XNRR2_4211), were up-regulated too (Fig. 5 ). In contrast, crotonyl-CoA...”
- “...6 ), and the expression of genes encoding for enzymes of this by-pass, isobutyryl-CoA mutase (XNRR2_1417, log 2 -fold 5.1) [ 35 ] and promiscuous acetyl-/propionyl-CoA carboxylases (e.g. XNRR2_4211/4212, log 2 -fold up to 4.7) was increased too (Fig. 6 , Table 1 ). It was...”
X551_02559 methylmalonyl-CoA mutase family protein from Methylibium sp. T29
43% identity, 71% coverage
Mpe_B0541 Methylmalonyl-CoA mutase from Methylibium petroleiphilum PM1
43% identity, 71% coverage
- Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary
Szabó, Standards in genomic sciences 2015 - “...Hydroxyisobutyraldehyde dehydrogenase Mpe_A0361 X551_03863 Partial homology 36 2-hydroxy-isobutyryl-CoA ligase Mpe_B0539 X551_02557 85 94 2-hydroxy-isobutyryl-CoA mutase Mpe_B0541 X551_02559 89 92 2-hydroxy-isobutyryl-CoA mutase C-terminal domain Mpe_B0538 X551_02556 86 91 3-hydroxybutyryl-CoA dehydrogenase Mpe_B0547 X551_02564 79 84 Acetyl-CoA acetyltransferase Mpe_A3367 X551_00431 Partial homology 45 Abbreviations MTBE Methyl tert -butyl ether...”
- Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase
Kurteva-Yaneva, The Journal of biological chemistry 2015 - “...sequences from Methylibium petroleiphilum PM1 ((MPetro) Mpe_B0541), Methylibium sp. T29 ((Methyl) EWS54629), Rhodobacter sphaeroides KD131 ((Rs) RSKD131_3116),...”
- Thermophilic Coenzyme B12-Dependent Acyl Coenzyme A (CoA) Mutase from Kyrpidia tusciae DSM 2912 Preferentially Catalyzes Isomerization of (R)-3-Hydroxybutyryl-CoA and 2-Hydroxyisobutyryl-CoA
Weichler, Applied and environmental microbiology 2015 - “...from A. tertiaricarbonis L108 (AFK77668), M. petroleiphilum PM1 (Mpe_B0541), R. sphaeroides ATCC Weichler et al. sequences of HCM and RCM significantly deviate...”
- “...clusters from M. petroleiphilum PM1 (Mpe_B0537 to Mpe_B0541), R. sphaeroides ATCC 17029 (Rsph17029_3649 to Rsph17029_3657), S. novella DSM 506 (Snov_2774 to...”
- Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA
Yaneva, The Journal of biological chemistry 2012 - “...with orthologous sequences from M. petroleiphilum PM1 (Mpe_B0541), R. sphaeroides KD131 (RSKD131_3116), R. sphaeroides ATCC 17029 (Rsph17029_3657), S. novella...”
- Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol
Hristova, Applied and environmental microbiology 2007 - “...Mpe_B0601 Mpe_B0558 Mpe_A2443 Mpe_B0555 Mpe_B0554 Mpe_B0561 Mpe_A0361 Mpe_B0539 Mpe_B0541 Mpe_B0538 Mpe_B0547 Mpe_A3367 1.5 NDa ND ND 12.4 5.2 11.6 4.3 4.6 1.4...”
hcmA / I3VE77 2-hydroxyisobutanoyl-CoA mutase large subunit (EC 5.4.99.64) from Aquincola tertiaricarbonis (see 3 papers)
HCMA_AQUTE / I3VE77 2-hydroxyisobutanoyl-CoA mutase large subunit; 2-hydroxyisobutyryl-CoA mutase large subunit; HCM large subunit; EC 5.4.99.64 from Aquincola tertiaricarbonis (see 2 papers)
I3VE77 2-hydroxyisobutanoyl-CoA mutase (subunit 2/2) (EC 5.4.99.64) from Aquincola tertiaricarbonis (see 3 papers)
43% identity, 71% coverage
- function: Together with HcmB, catalyzes the isomerization of 2- hydroxyisobutyryl-CoA and 3-hydroxybutyryl-CoA. Is specific for 2- hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA, and shows only very low activity with (R)-3-hydroxybutyryl-CoA, isobutyryl-CoA and butyryl- CoA (PubMed:22433853, PubMed:25720495). In vitro, can isomerize pivalyl-CoA and isovaleryl-CoA, with much lower efficiency (PubMed:25720495). Plays a central role in the degradation of substrates bearing a tert-butyl moiety, such as the fuel oxygenate methyl tert-butyl ether (MTBE) and its metabolites (PubMed:22433853).
catalytic activity: 2-hydroxyisobutanoyl-CoA = (3S)-3-hydroxybutanoyl-CoA (RHEA:49592)
subunit: Homotetramer composed of two large substrate-binding subunits (HcmA) and two small cobalamin-binding subunits (HcmB).
disruption phenotype: Insertion mutant cannot grow on 2- hydroxyisobutyric acid (2-HIBA).
4r3uA / I3VE77 Crystal structure of 2-hydroxyisobutyryl-coa mutase (see paper)
43% identity, 71% coverage
- Ligands: 3-hydroxybutanoyl-coenzyme a; s-{(3r,5r,9r)-1-[(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate; cobalamin (4r3uA)
icmA / CAB40912.1 isobutyryl-CoA mutase A from Streptomyces coelicolor (see paper)
SCO5415 isobutyryl-CoA mutase A from Streptomyces coelicolor A3(2)
43% identity, 72% coverage
Caur_1844 methylmalonyl-CoA mutase, large subunit from Chloroflexus aurantiacus J-10-fl
45% identity, 69% coverage
- Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Tang, BMC genomics 2011 - “...accD (Caur_1648), accB (Caur_3739), mcr (Caur_2614), pcs (Caur_ 0613), pccB (Caur_2034, Caur_3435), mcee (Caur_3037), mut (Caur_1844, Caur_2508, Caur_2509), smtA (Caur_0179), smtB (Caur_0178), sdhBAC (Caur_1880 to Caur_1882), fh (Caur_1443), mcl (Caur_0174), mch (Caur_0173), mct (Caur_0174), meh (Caur_0180) Glycolate assimilation and glyoxylate cycle glcDEF (Caur_1144 - 1145, Caur_2133,...”
- “...(5) methylmalonyl-CoA epimerase ( mcee , Caur_3037), (6) L -methylmalonyl-CoA mutase (MCM) ( mut , Caur_1844, Caur_2508, Caur_2509), (7) succinyl-CoA:( S )-malyl-CoA transferase ( smtA (Caur_0179), smtB (Caur_0178)), (8) succinate dehydrogenase ( sdhBAC , Caur_1880 to Caur_1882), (9) fumarate hydratase ( fh , Caur_1443), (10) (...”
MSMEG_4881 methylmalonyl-CoA mutase, N-terminus of large subunit from Mycobacterium smegmatis str. MC2 155
44% identity, 72% coverage
LIC_20058 methylmalonyl-CoA mutase family protein from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
LB074 methylmalonyl-CoA mutase from Leptospira interrogans serovar lai str. 56601
36% identity, 88% coverage
- Pathogenic Leptospires Modulate Protein Expression and Post-translational Modifications in Response to Mammalian Host Signals
Nally, Frontiers in cellular and infection microbiology 2017 - “...analysis (for proteins of unknown function) 313 0.00057 7.05 gi|45602612 ( AAS72087.1 ) methylmalonyl-CoA mutase (LIC_20058) 992, 987 0.000076, 0.000011 4.49, 3.71 gi|45601096 ( AAS70579.1 ) succinate dehydrogenase iron-sulfur subunit (LIC_12003) 375, 383, 379 0.0012, 0.017, 0.0015 3.95, 2.59, 2.48 gi|45600451 ( AAS69936.1 ) GroEL (LIC_11335)...”
- A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans
Eshghi, Infection and immunity 2014 - “...la0964 la2035 la0906 la1464 la3173 la3392 la3064 la4167 la0693 la2988 lb074 la4026 la3139 la2987 3.4 3.2 2.7 2.7 2.3 2.3 2.3 2.3 2.2 2.1 2.1 2.1 2.1 2.1 2.1...”
LIMLP_18125 methylmalonyl-CoA mutase family protein from Leptospira interrogans serovar Manilae
35% identity, 88% coverage
SRIMR7_07230 protein meaA from Streptomyces rimosus subsp. rimosus
36% identity, 89% coverage
SAM23877_RS28815 protein meaA from Streptomyces ambofaciens ATCC 23877
36% identity, 89% coverage
Q2RPT8 Methylmalonyl-CoA mutase from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
Rru_A3062 Methylmalonyl-CoA mutase-like from Rhodospirillum rubrum ATCC 11170
36% identity, 86% coverage
- Study of the Production of Poly(Hydroxybutyrate-co-Hydroxyhexanoate) and Poly(Hydroxybutyrate-co-Hydroxyvalerate-co-Hydroxyhexanoate) in Rhodospirillum rubrum
Cabecas, Applied and environmental microbiology 2022 (secret) - Genetic Plasticity and Ethylmalonyl Coenzyme A Pathway during Acetate Assimilation in Rhodospirillum rubrum S1H under Photoheterotrophic Conditions
De, Applied and environmental microbiology 2018 - “...1.19 No. of identified peptidesc 5 6 3 Q2RPT8 Q2RPT6 Q2RV43 Q2RXX3 Q2RV44 Q2RYD8 Q2RYD7 Q2RRG6 Rru_A3062 Rru_A3064 Rru_A1201 Rru_A0217 Rru_A1200 Rru_A0052...”
- The metabolic pathways of carbon assimilation and polyhydroxyalkanoate production by Rhodospirillum rubrum in response to different atmospheric fermentation
Tang, PloS one 2024 - “...synthase 4.49E-15 5.863 8.30E-11 2.855 ethylmalony-CoA (EMC) pathway Rru_A1201 Mesaconyl-CoA hydratase ND ND 0.00013 0.8 Rru_A3062 Methylmalonyl-CoA mutase 1.63E-08 1.338 1.21E-16 1.947 Rru_A3063 Crotonyl-CoA carboxylase/reductase 2.38E-08 1.800 3.65E-54 3.723 Rru_A3064 Isovaleryl-CoA dehydrogenase: Acyl-CoA dehydrogenase ND ND 4.74E-11 1.429 pyruvate ferredoxin oxidoreductase (PFOR) Rru_A2398 Pyruvate- flavodoxin oxidoreductase...”
- “...[ 27 , 28 ]. Besides Rubisco other carboxylases belonging to enthylmalony-CoA (EMC) pathway ( Rru_A3062 , p = 1.63E-08, fold change = 1.338; Rru_A3063 , p = 2.38E-08, fold change = 1.800) also participates in the assimilation of catalytic CO 2 . Those are consistent...”
- Effects of Mixing Volatile Fatty Acids as Carbon Sources on Rhodospirillum rubrum Carbon Metabolism and Redox Balance Mechanisms
Cabecas, Microorganisms 2021 - “...under butyrate conditions, as was the cluster of key enzymes involved in the EMC pathway (Rru_A3062, fold change: 2.62; Rru_A3063, fold change: 6.17; Rru_3064, fold change: 2.23) ( Table 1 ). A higher abundance of proteins involved in the newly proposed MBC pathway, which combined branched-chain...”
- “...during the butyrate assimilation phase. Indeed, the cluster of key enzymes of the EMC pathway (Rru_A3062, Rru_A3063, Rru_A3064) was no longer upregulated during the assimilation of butyrate ( Table 1 ). Comparing butyrate only conditions with the butyrate assimilation phase under binary mixture conditions, these three...”
- New perspectives on butyrate assimilation in Rhodospirillum rubrum S1H under photoheterotrophic conditions
De, BMC microbiology 2020 - “...Rru_A1572 Ethylmalonyl-CoA/Methylmalonyl-CoA epimerase 0.9 6e-01 5 1.4 2e-02 0.5 1e-04 2.3 6e-07 0.7 3e-03 4 Rru_A3062 Methylmalonyl-CoA mutase (EC 5.4.99.2) 3.7 2e-03 3 1.0 8e-01 1.3 5e-01 1.4 3e-01 1.0 8e-01 2 Rru_A3064 Methylsuccinyl-CoA dehydrogenase 1.5 2e-03 6 0.8 1e-02 0.9 3e-01 1.1 1e+00 1.6 3e-05...”
- “...0.41 2e-02 Rru_A3063 Crotonyl-CoA carboxylase/reductase 0.15 0.18 7e-01 Rru_A1572 a Ethylmalonyl-CoA/Methylmalonyl-CoA epimerase n.a. n.a. n.a. Rru_A3062 Methylmalonyl-CoA mutase (EC 5.4.99.2) 0.02 1.77 5e-04 Rru_A3064 Methylsuccinyl-CoA dehydrogenase 0.01 2.3 1e-03 Rru_A1201 Mesaconyl-CoA hydratase 0.06 3.42 2e-07 Rru_A0217 L-Malyl-CoA/b-methylmalyl-CoA lyase 0.05 3.11 1e-05 Rru_A1200 b Malyl-CoA thioesterase n.a....”
- Global Proteomic Analysis Reveals High Light Intensity Adaptation Strategies and Polyhydroxyalkanoate Production in Rhodospirillum rubrum Cultivated With Acetate as Carbon Source
Bayon-Vicente, Frontiers in microbiology 2020 - “...for key enzymes of the ethylmalonyl-CoA pathway [i.e., crotonyl-CoA carboxylase/reductase (Rru_A3063), (2 R )-ethylmalonyl-CoA mutase (Rru_A3062), and methylsuccinyl-CoA dehydrogenase (Rru_A3064)]. Proteomic analysis revealed a higher abundance of the corresponding enzymes, but also of most of the proteins of the amplified gene cluster. The resulting phenotype showed...”
- “...) upregulation of the key enzyme of the EMC pathway [crotonyl-CoA carboxylase/reductase (Rru_A3063), ethylmalonyl-CoA mutase (Rru_A3062) and methylsuccinyl-CoA dehydrogenase (Rru_A3064)] in the acetate-competent strain increases the flux through the EMC pathway, thus consuming excess of reduced cofactors. The EMC pathway has already been proposed to play...”
- Photoheterotrophic Assimilation of Valerate and Associated Polyhydroxyalkanoate Production by Rhodospirillum rubrum
Bayon-Vicente, Applied and environmental microbiology 2020 (secret) - Genetic Plasticity and Ethylmalonyl Coenzyme A Pathway during Acetate Assimilation in Rhodospirillum rubrum S1H under Photoheterotrophic Conditions
De, Applied and environmental microbiology 2018 - “...Rru_A0467 Rru_A0468 Rru_A0469 Rru_A1786 Rru_A1040 Rru_A3062 Rru_A3064 Rru_A1201 Rru_A0217 Rru_A1200b Rru_A0052 Rru_A0053 Rru_A2479 Locus Ethylmalonyl-CoA...”
- “...and Environmental Microbiology t 1 Ccr_Fw Fg Ccr_Rv A Wild Type rru_A3062 ccr C H.R.2 Fgt 2 Km_Fw R ccr::Km H.R.1 B rru_A3064 KmR R Km Cass. Fgt.1 (525 bp)...”
AMED_7761 protein meaA from Amycolatopsis mediterranei U32
36% identity, 86% coverage
- A preliminary study of the mechanism of nitrate-stimulated remarkable increase of rifamycin production in Amycolatopsis mediterranei U32 by RNA-seq
Shao, Microbial cell factories 2015 - “...are totally four mcm genes annotated in U32, including AMED_0913 , AMED_0914 , AMED_2498 and AMED_7761 , among which AMED_2498 was apparently transcriptionally repressed by as much as 25 folds after the addition of nitrate while the transcription of others was almost unchanged in ES phase...”
- “...overproducer of rifamycin B, significantly increased the yield [ 29 ]. Notably, the mutB2 homologue, AMED_7761 kept an extremely low transcriptional level in U32, which may account for the high yield of rifamycin SV. Moreover, the transcription of mce was up-regulated 1.4 folds upon addition of...”
D5WTR7 2-hydroxyisobutanoyl-CoA mutase (subunit 2/2) (EC 5.4.99.64) from Kyrpidia tusciae DSM 2912 (see paper)
38% identity, 76% coverage
D2SEQ5 methylmalonyl-CoA mutase from Geodermatophilus obscurus (strain ATCC 25078 / DSM 43160 / JCM 3152 / CCUG 61914 / KCC A-0152 / KCTC 9177 / NBRC 13315 / NRRL B-3577 / G-20)
35% identity, 87% coverage
C7C6S9 ethylmalonyl-CoA mutase (EC 5.4.99.63) from Methylorubrum extorquens (see paper)
36% identity, 86% coverage
ECM_METEA / Q49115 Ethylmalonyl-CoA mutase; EC 5.4.99.63 from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (Methylobacterium extorquens) (see 3 papers)
36% identity, 86% coverage
- function: Radical enzyme that catalyzes the transformation of (2R)- ethylmalonyl-CoA to (2S)-methylsuccinyl-CoA (PubMed:25448820). Is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation required for M.extorquens growth on one- and two-carbon compounds such as ethylamine, methanol or ethanol as sole carbon source (PubMed:25448820, PubMed:8704985, PubMed:8868443). This enzyme acts as a regulatory metabolic control point in this pathway, that allows M.extorquens to efficiently restore metabolic balance when challenged with a sudden change in the growth substrate (PubMed:25448820).
catalytic activity: (2R)-ethylmalonyl-CoA = (2S)-methylsuccinyl-CoA (RHEA:45576)
cofactor: adenosylcob(III)alamin
disruption phenotype: Cells lacking this gene lose the ability to grow on C1 (methanol and methylamine) and C2 (ethanol and ethylamine) compounds, and also on beta-hydroxybutyrate, but they grow normally on pyruvate. Growth on C1 and C2 compounds is restored by addition of glyoxylate or glycolate, indicating that these mutants are unable to convert acetyl-CoA into glyoxylate.
GL4_3338 protein meaA from Methyloceanibacter caenitepidi
35% identity, 86% coverage
- Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Takeuchi, PloS one 2019 - “...Methylsuccinyl-CoA dehydrogenase mcd 283 293 0.05 0.593 GL4_2084 Methylmalonyl-CoA epimerase Mcee 173 165 -0.06 0.430 GL4_3338 Ethylmalonyl-CoA mutase ecm 161 218 0.43 0.000 GL4_0095 Mesaconyl-CoA hydratase mch 188 181 -0.05 0.367 GL4_3371 malyl-CoA lyase mcl1 971 638 -0.61 0.000 GL4_0468 L-malyl-CoA/beta-methylmalyl-CoA lyase mcl2 50 237 2.22...”
- “...( hbdA ; GL4_3328), crotonyl-CoA carboxylase/reductase ( ccr ; GL4_3337), ethylmalonyl-CoA mutase ( ecm ; GL4_3338) and l -malyl-CoA/beta-methylmalyl-CoA lyase ( mcl2 ; GL4_0468) [ 27 ] were significantly upregulated ( Fig 3 , Table 1 ). In the TCA cycle, genes for citrate synthase (...”
CC_3081 methylmalonyl-CoA mutase, alpha subunit from Caulobacter crescentus CB15
CCNA_03177 methylmalonyl-CoA mutase MeaA-like protein from Caulobacter crescentus NA1000
36% identity, 88% coverage
- Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...protein 3.21 CC_1754 b CCNA_01830 TonB-dependent receptor 2.07 CC_2389 CCNA_02472 Cobalt-zinc-cadmium resistance protein czcB 2.42 CC_3081 CCNA_03177 Methylmalonyl-CoA mutase MeaA-like protein 2.55 CC_3127 b CCNA_03227 TonB-dependent receptor 2.41 CC_3413 CCNA_03524 Di-/tripeptide transporter (Major Facilitator Superfamily) 2.48 CC_3461 b CCNA_03574 TonB-dependent receptor 2.70 Hypothetical CC_0600 CCNA_00636 Hypothetical...”
- Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B12 Scavenging
Aretakis, mSystems 2019 - “...for nucleotide reduction, NrdJ (CCNA_01966), NrdE (CCNA_03607), and NrdB (CCNA_00261). Pathway for succinyl-CoA biosynthesis, MeaA (CCNA_03177) and MutB (CCNA_02459). Square boxes next to each enzyme contain an orange heat map which represents the fraction of ribosome footprints. ADO (adenosyl) and CN (cyano) refer to the B...”
- Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...3.21 CC_1754 b CCNA_01830 TonB-dependent receptor 2.07 CC_2389 CCNA_02472 Cobalt-zinc-cadmium resistance protein czcB 2.42 CC_3081 CCNA_03177 Methylmalonyl-CoA mutase MeaA-like protein 2.55 CC_3127 b CCNA_03227 TonB-dependent receptor 2.41 CC_3413 CCNA_03524 Di-/tripeptide transporter (Major Facilitator Superfamily) 2.48 CC_3461 b CCNA_03574 TonB-dependent receptor 2.70 Hypothetical CC_0600 CCNA_00636 Hypothetical protein...”
ECM_CERS4 / Q3IZ90 Ethylmalonyl-CoA mutase; EC 5.4.99.63 from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (Rhodobacter sphaeroides) (see paper)
Q3IZ90 ethylmalonyl-CoA mutase (EC 5.4.99.63) from Cereibacter sphaeroides (see paper)
RSP_0961 similiar to methylmalonyl-CoA mutases from Rhodobacter sphaeroides 2.4.1
37% identity, 86% coverage
- function: Radical enzyme that catalyzes the transformation of (2R)- ethylmalonyl-CoA to (2S)-methylsuccinyl-CoA. Is involved in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation required for R.sphaeroides growth on acetate as sole carbon source. Is highly specific for its substrate, ethylmalonyl-CoA, and accepts methylmalonyl-CoA only at 0.2% relative activity.
catalytic activity: (2R)-ethylmalonyl-CoA = (2S)-methylsuccinyl-CoA (RHEA:45576)
cofactor: adenosylcob(III)alamin
subunit: Homodimer.
disruption phenotype: Cells lacking this gene are able to grow with carbon substrates that do not require the operation of the (complete) ethylmalonyl-CoA pathway (succinate, propionate/HCO3(-), or acetate plus glyoxylate) but are unable to use acetate or acetoacetate as the sole carbon source. They show undetectable ethylmalonyl-CoA mutase activity when grown with acetate plus glyoxylate, while are still able to convert methylmalonyl-CoA to succinyl-CoA. - Construction of a Rhodobacter sphaeroides Strain That Efficiently Produces Hydrogen Gas from Acetate without Poly(β-Hydroxybutyrate) Accumulation: Insight into the Role of PhaR in Acetate Metabolism
Shimizu, Applied and environmental microbiology 2022 (secret) - Barriers to 3-Hydroxypropionate-Dependent Growth of Rhodobacter sphaeroides by Distinct Disruptions of the Ethylmalonyl Coenzyme A Pathway
Carlson, Journal of bacteriology 2019 - “...pKB22 employed for the markerless in-frame deletion of ecm (rsp_0961) was constructed by amplifying 12 bp of the 5= ecm coding region plus 1,434 bp directly...”
- Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans
Kremer, mBio 2019 - “...RSP_0747 Pden_2027 Crotonyl-CoA carboxylase/reductase ccr RSP_0960 Pden_3873 Ethylmalonyl-CoA/methylmalonyl-CoA epimerase epi RSP_0812 Pden_2178 Ethylmalonyl-CoA mutase ecm RSP_0961 Pden_3875 ( 2S )-MethylsuccinylCoA dehydrogenase mcd RSP_1679 Pden_2840 Mesaconyl-CoA hydratase mch RSP_0973 Pden_0566 -MethylmalylCoA/ l -malylCoA lyase mcl-1 RSP_1771 Pden_0799 ( S )-MalylCoA thioesterase mcl-2 RSP_0970 Pden_0563 Propionyl-CoA carboxylase pccAB...”
- In vivo analysis of cobinamide salvaging in Rhodobacter sphaeroides strain 2.4.1
Gray, Journal of bacteriology 2009 - “...required for growth on acetate (MeaA, locus tag RSP_0961; McmA, locus tag RSP_2192, respectively) (1, 22, 23), methionine synthase (MetH, locus tag RSP_3346)...”
PDEN_RS19280 protein meaA from Paracoccus denitrificans PD1222
36% identity, 86% coverage
Pden_3875 methylmalonyl-CoA mutase, large subunit from Paracoccus denitrificans PD1222
36% identity, 86% coverage
Caur_2509 / A9WI24 methylmalonyl-CoA mutase small subunit (EC 5.4.99.2) from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (see paper)
Caur_2509 methylmalonyl-CoA mutase, large subunit from Chloroflexus aurantiacus J-10-fl
32% identity, 94% coverage
- Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
Tang, BMC genomics 2011 - “...accB (Caur_3739), mcr (Caur_2614), pcs (Caur_ 0613), pccB (Caur_2034, Caur_3435), mcee (Caur_3037), mut (Caur_1844, Caur_2508, Caur_2509), smtA (Caur_0179), smtB (Caur_0178), sdhBAC (Caur_1880 to Caur_1882), fh (Caur_1443), mcl (Caur_0174), mch (Caur_0173), mct (Caur_0174), meh (Caur_0180) Glycolate assimilation and glyoxylate cycle glcDEF (Caur_1144 - 1145, Caur_2133, Caur_2135), glyr...”
- “...epimerase ( mcee , Caur_3037), (6) L -methylmalonyl-CoA mutase (MCM) ( mut , Caur_1844, Caur_2508, Caur_2509), (7) succinyl-CoA:( S )-malyl-CoA transferase ( smtA (Caur_0179), smtB (Caur_0178)), (8) succinate dehydrogenase ( sdhBAC , Caur_1880 to Caur_1882), (9) fumarate hydratase ( fh , Caur_1443), (10) ( S )-malyl-CoA/-methylmalyl-CoA/(...”
PFJ30894_RS04255 methylmalonyl-CoA mutase family protein from Phascolarctobacterium faecium
28% identity, 97% coverage
PCMA_XANP2 / A7IQE5 Pivalyl-CoA mutase large subunit; PCM large subunit; Pivalyl-CoA mutase, substrate-binding subunit; EC 5.4.99.- from Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (see paper)
34% identity, 71% coverage
- function: Together with Xaut_5044, catalyzes the reversible isomerization between pivalyl-CoA and isovaleryl-CoA, using radical chemistry. Does not exhibit isobutyryl-CoA mutase (ICM) activity.
catalytic activity: 3-methylbutanoyl-CoA = 2,2-dimethylpropanoyl-CoA (RHEA:52620)
subunit: Homodimer in the absence of the PCM small subunit. Weakly interacts with the PCM small subunit; an alpha(2)beta(2) stoichiometry seems to represent the active state of the enzyme.
AMED_2498 fused isobutyryl-CoA mutase/GTPase IcmF from Amycolatopsis mediterranei U32
33% identity, 46% coverage
ICMF_GEOKA / Q5KUG0 Fused isobutyryl-CoA mutase; EC 5.4.99.13; EC 3.6.5.- from Geobacillus kaustophilus (strain HTA426) (see 2 papers)
GK3391 hypothetical protein from Geobacillus kaustophilus HTA426
34% identity, 46% coverage
- function: Catalyzes the reversible interconversion of isobutyryl-CoA and n-butyryl-CoA, and to a lesser extent, of pivalyl-CoA and isovaleryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly. Also displays ATPase activity. Is not able to convert 3- hydroxybutyryl-CoA to 2-hydroxyisobutyryl-CoA. Does not exhibit methylmalonyl-CoA mutase (MCM) activity.
catalytic activity: 2-methylpropanoyl-CoA = butanoyl-CoA (RHEA:13141)
catalytic activity: 3-methylbutanoyl-CoA = 2,2-dimethylpropanoyl-CoA (RHEA:52620)
catalytic activity: GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)
cofactor: adenosylcob(III)alamin
cofactor: Mg(2+)
subunit: Homodimer. - Bacterial acyl-CoA mutase specifically catalyzes coenzyme B12-dependent isomerization of 2-hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA
Yaneva, The Journal of biological chemistry 2012 - “...AAC08713), IcmF from Geobacillus kaustophilus HTA426 (GK3391), MCM from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1 (YP_003687736), and ECM from...”
WP_065525509 fused isobutyryl-CoA mutase/GTPase IcmF from Planococcus donghaensis
34% identity, 46% coverage
ICMF_PARXL / Q146L7 Fused isobutyryl-CoA mutase; EC 5.4.99.13; EC 3.6.5.- from Paraburkholderia xenovorans (strain LB400) (see paper)
34% identity, 39% coverage
- function: Catalyzes the reversible interconversion of isobutyryl-CoA and n-butyryl-CoA, using radical chemistry (PubMed:19864421). Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly (By similarity). Does not exhibit methylmalonyl- CoA mutase (MCM) activity (PubMed:19864421).
catalytic activity: 2-methylpropanoyl-CoA = butanoyl-CoA (RHEA:13141)
catalytic activity: GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)
cofactor: adenosylcob(III)alamin
cofactor: Mg(2+)
subunit: Homodimer.
RSIPO_00260 methylmalonyl-coa mutase protein from Ralstonia solanacearum IPO1609
34% identity, 47% coverage
BMMGA3_RS15615 fused isobutyryl-CoA mutase/GTPase IcmF from Bacillus methanolicus MGA3
33% identity, 46% coverage
Q8Y2U5 methylmalonyl-CoA mutase (EC 5.4.99.2) from Ralstonia solanacearum (see paper)
34% identity, 47% coverage
ICMF_CUPMC / Q1LRY0 Fused isobutyryl-CoA mutase; EC 5.4.99.13; EC 3.6.5.- from Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) (Ralstonia metallidurans) (see 3 papers)
Q1LRY0 isobutyryl-CoA mutase (EC 5.4.99.13) from Cupriavidus metallidurans (see 3 papers)
34% identity, 45% coverage
- function: Catalyzes the reversible interconversion of isobutyryl-CoA and n-butyryl-CoA, and to a much lesser extent, of pivalyl-CoA and isovaleryl-CoA, using radical chemistry (PubMed:22167181). Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly (PubMed:22167181, PubMed:25675500). The G-domain of IcmF has also a role in its cofactor repair (PubMed:28130442). Does not display ATPase activity.
catalytic activity: 2-methylpropanoyl-CoA = butanoyl-CoA (RHEA:13141)
catalytic activity: 3-methylbutanoyl-CoA = 2,2-dimethylpropanoyl-CoA (RHEA:52620)
catalytic activity: GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)
cofactor: adenosylcob(III)alamin
cofactor: Mg(2+)
subunit: Homodimer.
8sslA / Q1LRY0 Isobutyryl-coa mutase fused q341a in the presence of gtp (see paper)
34% identity, 46% coverage
- Ligands: guanosine-5'-diphosphate; magnesium ion (8sslA)
H16_A0280 fused isobutyryl-CoA mutase/GTPase IcmF from Cupriavidus necator H16
H16_A0280 Methylmalonyl-CoA mutase from Ralstonia eutropha H16
34% identity, 45% coverage
- Investigations on the microbial catabolism of the organic sulfur compounds TDP and DTDP in Ralstonia eutropha H16 employing DNA microarrays
Peplinski, Applied microbiology and biotechnology 2010 - “...synthetase 17.01 19.93 3.29 2.31 H16_A0234 aidB Acyl-CoA dehydrogenase, short-chain specific 2.78 2.65 3.35 x H16_A0280 sbml Methylmalonyl-Coa mutase 9.72 6.11 4.05 x H16_A1949 sbm2 Methylmalonyl-Coa mutase 248.35 2.87 7.00 x H16_A2251 phaY1 d -()-3-hydroxybutyrate oligomer hydrolase 3.07 3.79 9.93 x H16_B1192 Acyl-CoA dehydrogenase 25.89 77.24...”
- “...further genes involved in propionate metabolism were detected, encoding a methylmalonyl-CoA mutase ( sbm1 , H16_A0280, four to tenfold; sbm2 , H16_A1949, 3- to 248-fold). This enzyme converts succinyl-CoA to methylmalonyl-CoA. Finally, genes for an ABC-type transporter of the NitT family (H16_A0357-A0359, 6- to 130-fold) exhibited...”
ICMF_NOCFA / Q5Z110 Fused isobutyryl-CoA mutase; EC 5.4.99.13; EC 3.6.5.- from Nocardia farcinica (strain IFM 10152) (see paper)
33% identity, 46% coverage
- function: Catalyzes the reversible interconversion of isobutyryl-CoA and n-butyryl-CoA, using radical chemistry (PubMed:19864421). Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly (By similarity). Does not exhibit methylmalonyl- CoA mutase (MCM) activity (PubMed:19864421).
catalytic activity: 2-methylpropanoyl-CoA = butanoyl-CoA (RHEA:13141)
catalytic activity: GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)
cofactor: adenosylcob(III)alamin
cofactor: Mg(2+)
subunit: Homodimer.
Amuc_1984 Methylmalonyl-CoA mutase from Akkermansia muciniphila ATCC BAA-835
27% identity, 94% coverage
GOZ73_RS10915 methylmalonyl-CoA mutase family protein from Akkermansia muciniphila
27% identity, 94% coverage
Q2RRG5 methylmalonyl-CoA mutase from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)
Rru_A2480 Methylmalonyl-CoA mutase from Rhodospirillum rubrum ATCC 11170
28% identity, 78% coverage
- Study of the Production of Poly(Hydroxybutyrate-co-Hydroxyhexanoate) and Poly(Hydroxybutyrate-co-Hydroxyvalerate-co-Hydroxyhexanoate) in Rhodospirillum rubrum
Cabecas, Applied and environmental microbiology 2022 (secret) - Effects of Mixing Volatile Fatty Acids as Carbon Sources on Rhodospirillum rubrum Carbon Metabolism and Redox Balance Mechanisms
Cabecas, Microorganisms 2021 - “...confirming the previous reports [ 18 ]. This pathway requires five enzymes (Rru_A0052, Rru_A0053, Rru_A1572, Rru_A2480, Rru_A1927), among which three were significantly more abundant in propionate conditions than in butyrate conditions: the biotin carboxylase (Rru_A0052, fold change: 0.63), the methylmalonyl-CoA mutase (Rru_A2480, fold change: 0.61), and...”
- “...epimerase tr|Q2RRG6 Rru_A2479 0.72 8.21 10 2 1.75 9.56 10 2 6 Methylmalonyl-CoA mutase tr|Q2RRG5 Rru_A2480 0.61 3.43 10 2 1.56 1.37 10 3 6 Methylmalonyl-CoA mutase Methilcitrate cycle tr|Q2RRX7 Rru_A2318 0.76 4.60 10 1 0.47 1.22 10 2 4 2-methylcitrate dehydratase tr|Q2RRX6 Rru_A2319 0.25 1.61...”
- Photoheterotrophic Assimilation of Valerate and Associated Polyhydroxyalkanoate Production by Rhodospirillum rubrum
Bayon-Vicente, Applied and environmental microbiology 2020 (secret)
SNOD_RS26855 fused isobutyryl-CoA mutase/GTPase IcmF from Streptomyces nodosus
32% identity, 46% coverage
- Comparative Transcriptome Analysis of Streptomyces nodosus Mutant With a High-Yield Amphotericin B
Huang, Frontiers in bioengineering and biotechnology 2020 - “...2-oxoglutarate dehydrogenase. (n) SNOD_RS04655 succinate dehydrogenase. (o) SNOD_RS20250 propionyl-CoA carboxylase. (p) SNOD_RS22165 methylmalonyl-CoA epimerase. (q) SNOD_RS26855 methylmalonyl-CoA mutase. As acetyl-CoA enters the tricarboxylic acid cycle (TCA), the expression of SNOD _RS14500 gene (citrate synthase) and unlabeled gene 2 (2-oxoglutarate dehydrogenase) was upregulated by 1.1-fold (log 2...”
SACE_5638 methylmalonyl-CoA mutase, beta subunit from Saccharopolyspora erythraea NRRL 2338
32% identity, 63% coverage
- Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in Saccharopolyspora erythraea
Wu, Journal of biological engineering 2019 - “...; fumarate reductase iron-sulfur subunit, SACE_1171 ; malate dehydrogenase, SACE_3674 ; methylmalonyl-CoA mutase subunit beta, SACE_5638 ; methylmalonyl-CoA mutase, SACE_5639 ; succinyl-CoA synthetase subunit alpha, SACE_6668 ; succinyl-CoA synthetase subunit beta, SACE_6669 ; phosphoenolpyruvate carboxykinase, SACE_7274 ) were analyzed by qRT-PCR. Compared to A226, SACE_1171 was...”
- Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains
Li, BMC genomics 2013 - “...pathways such as carboxylation of propionyl-CoA and rearrangement of succinyl-CoA. The mutA and mutB genes (SACE_5638, 5639) encode methylmalonyl-CoA mutase (MCM), which catalyzes the reversible isomerization of succinyl-CoA and methymalonyl-CoA. Reeves et al. have proposed a metabolic model where in carbohydrate-based fermentations MCM acts as a...”
BT_2091 methylmalonyl-CoA mutase small subunit from Bacteroides thetaiotaomicron VPI-5482
29% identity, 63% coverage
LBJ_RS11290 methylmalonyl-CoA mutase family protein from Leptospira borgpetersenii serovar Hardjo-bovis str. JB197
30% identity, 44% coverage
ING2E5A_1515 methylmalonyl-CoA mutase small subunit from Petrimonas mucosa
29% identity, 72% coverage
- The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses
Maus, Microorganisms 2020 - “...ING2E5A_1055, ING2E5A_1054 1.2.4.2, 2.3.1.61 Oxoglutarate dehydrogenase (succinyl-transferring), Dihydrolipoyllysine-residue succinyltransferase 2-oxoglutarate succinyl-CoA suc A, suc B ING2E5A_1515, ING2E5A_1517 5.4.99.2 Methylmalonyl-CoA mutase ( R )-methylmalonyl-CoA <=> succinyl-CoA mut A, mut B ING2E5A_1046 5.1.99.1 Methylmalonyl-CoA epimerase ( R )-methylmalonyl-CoA <=> ( S )-2-Methylmalonyl-CoA ING2E5A_1045, ING2E5A_1864 6.4.1.3 Propionyl-CoA carboxylase ATP...”
Q8F222 methylmalonyl-CoA mutase (EC 5.4.99.2) from Leptospira interrogans serovar lai str. 56601 (see paper)
29% identity, 44% coverage
mutA / AAA03040.1 methylmalonyl-CoA small subunit from Streptomyces cinnamonensis (see paper)
29% identity, 62% coverage
PG1656 methylmalonyl-CoA mutase, small subunit from Porphyromonas gingivalis W83
PGN_0457 methylmalonyl-CoA mutase small subunit from Porphyromonas gingivalis ATCC 33277
28% identity, 60% coverage
- Characterisation of the Porphyromonas gingivalis Manganese Transport Regulator Orthologue
Zhang, PloS one 2016 - “...gingivalis W83 gDNA nt 1,371,9151,372,186 [ 32 ]). A 385 bp internal region of the PG1656 gene (C1; P . gingivalis W83 gDNA nt 1,737,9491,738,333 [ 32 ]) was amplified for use as a negative control in the EMSA. Biotinylated amplicons were produced using primers containing...”
- “...and Mn 2+ in the control of this regulator. A 385 bp internal fragment of PG1656 (C1) that encodes the methylmalonyl-CoA mutase small subunit was used as a negative DNA control to determine whether PgMntR binding to promoter-containing DNA was specific. As a start to test...”
- Post-translational Modifications in Oral Bacteria and Their Functional Impact
Ma, Frontiers in microbiology 2021 - “...). Furthermore, protein succinylation and acetylation were extensively overlapped in P. gingivalis , including PGN_0377, PGN_0457, PGN_0497, PGN_0723, PGN_0724, PGN_0725, PGN_1176, PGN_1178, PGN_1341, and PGN_1367, which play a crucial role in the ribosome and metabolic processes ( Zeng et al., 2020 ). S -glutathionylation is the...”
- A two-component system regulates hemin acquisition in Porphyromonas gingivalis
Scott, PloS one 2013 - “...x x PGN_0429 Putative 4-alpha-glucanotransferase xx x Intergenic PGN_0433/PGN_0434 Phosphoglycerate kinase/phosphoenolpyruvate carboxykinase xx x x PGN_0457 Methylmalonyl-CoA mutase small subunit xx xx x PGN_0556 Putative cobalamin biosynthesis-related protein x xx x PGN_0606 Glucosamine-6-phosphate deaminase-like protein xxx xx x PGN_1530 2-oxoglutarate ferredoxin oxidoreductase subunit xx x x...”
XNR_4666 methylmalonyl-CoA mutase family protein from Streptomyces albidoflavus
29% identity, 60% coverage
PFCIRM129_07235, PFREUD_07660 methylmalonyl-CoA mutase small subunit from Propionibacterium freudenreichii subsp. freudenreichii
27% identity, 67% coverage
7reqD / P11652 Methylmalonyl-coa mutase, 2-carboxypropyl-coa inhibitor complex (see paper)
27% identity, 67% coverage
- Ligand: 2-carboxypropyl-coenzyme a (7reqD)
MSMEG_3158 methylmalonyl-CoA mutase, small subunit from Mycobacterium smegmatis str. MC2 155
30% identity, 60% coverage
- De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis
Kipkorir, Journal of bacteriology 2021 - “...). TABLE 1 Predicted cobalamin-dependent enzymes in M. smegmatis Gene Annotation a Cofactor Reaction catalyzed MSMEG_3158 ( mutA ) Methylmalonyl-CoA mutase, small subunit AdoCbl Isomerization MSMEG_3159 ( mutB ) Methylmalonyl-CoA mutase large subunit AdoCbl MSMEG_0497 Glycerol dehydratase large subunit AdoCbl Isomerization MSMEG_1547 Glycerol dehydratase large subunit...”
- Dynamic Characterization of Protein and Posttranslational Modification Levels in Mycobacterial Cholesterol Catabolism
Xu, mSystems 2020 - “...and methylmalonyl pathway, including aconitate hydratase (MSMEG_3143), isocitrate lyase (MSMEG_0911), methylmalonyl-CoA epimerase (MSMEG_4921), methylmalonyl-CoA mutase (MSMEG_3158), methylisocitrate lyase (MSMEG_6646), and 2-methylcitrate dehydratase (MSMEG_6645), showed higher protein expression levels in the presence of cholesterol ( Fig.2B ). This result strongly suggested that cholesterol-derived acetyl-CoA and propionyl-CoA were...”
mutA / P11652 methylmalonyl-CoA mutase small subunit (EC 5.4.99.2) from Propionibacterium freudenreichii subsp. shermanii (see 8 papers)
P11652 methylmalonyl-CoA mutase (EC 5.4.99.2) from Propionibacterium freudenreichii subsp. shermanii (see paper)
27% identity, 67% coverage
- Novel B(12)-dependent acyl-CoA mutases and their biotechnological potential
Cracan, Biochemistry 2012 - “...on the right. The following proteins were used as examples: MCMs ( Propionibacterium shermanii ()(P11653, P11652), E. coli (2)(AAA69084), Metallosphaera sedula (22)(Msed_0638, Msed_2055) and Bacillus tusciae (22)(YP_003589181)); ICM ( Streptomyces cinnamonensis (22)(AAC08713, CAB59633)), IcmF ( Geobacillus kaustophilus (2)(YP_149244)), HCM ( Rhodobacter sphaeroides (22)(Rsph17029_3657, Rsph17029_3654)), and ECM...”
NCgl1472 methylmalonyl-CoA mutase family protein from Corynebacterium glutamicum ATCC 13032
27% identity, 65% coverage
AMED_0913 methylmalonyl-CoA mutase family protein from Amycolatopsis mediterranei U32
37% identity, 33% coverage
CRM90_15020 methylmalonyl-CoA mutase small subunit from Mycobacterium sp. ENV421
32% identity, 60% coverage
MMAR_2302 methylmalonyl-CoA mutase small subunit, MutA from Mycobacterium marinum M
30% identity, 60% coverage
Msil_3785 Methylmalonyl-CoA mutase from Methylocella silvestris BL2
27% identity, 62% coverage
- Genome Scale Metabolic Model of the versatile methanotroph Methylocella silvestris
Bordel, Microbial cell factories 2020 - “...the previously discussed oxidoreductase coded by the gene Msil_1641, and the methylmalonyl-CoA mutase coded by Msil_3785. The identified enzymes included also two enzymes of the serine cycle, namely phosphoenolpyruvate carboxylase (Msil_1718) and serine-glyoxylate aminotransferase (Msil_1714), which show their highest expression levels during growth on methane. 3-oxoacyl-synthase...”
GSU1578 B12-binding protein from Geobacter sulfurreducens PCA
53% identity, 18% coverage
- Cobalt Resistance via Detoxification and Mineralization in the Iron-Reducing Bacterium Geobacter sulfurreducens
Dulay, Frontiers in microbiology 2020 - “...Warren, 2012 ). We identified in a separate genomic location two additional cobamide biosynthetic enzymes, GSU1578 and CobA (GSU1577). Also unlinked were two genes encoding enzymes for the methylation (HemD, GSU3286) and oxidation (CysG, GSU3282) of uroporphyrinogen III, the common precursor of cobamide and heme biosynthesis...”
- “...into adenosyl cobinamide in sequential reactions initiated by an adenosylcobamide-binding subunit of an (R)-methylmalonyl-CoA mutase (GSU1578). The step catalyzed by CobU (GSU3010) generates an adenosine-GDP-cobinamide substrate for attachment of the cobamide lower ligand. G. sulfurreducens produces a cobamide with a 5-hydroxybenzimidazole (5-OHBza) lower ligand ( Figure...”
MAB_2712c Probable methylmalonyl-CoA mutase small subunit MutA from Mycobacterium abscessus ATCC 19977
36% identity, 34% coverage
BCG_1555 putative methylmalonyl-CoA mutase small subunit mutA from Mycobacterium bovis BCG str. Pasteur 1173P2
NP_216008 methylmalonyl-CoA mutase small subunit from Mycobacterium tuberculosis H37Rv
Rv1492 PROBABLE METHYLMALONYL-CoA MUTASE SMALL SUBUNIT MUTA (MCM) from Mycobacterium tuberculosis H37Rv
29% identity, 60% coverage
- Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages
Flores-Valdez, Scientific reports 2024 - “...0.6089 0.006884392 arsB2 BCG_3643 Rv3578 Possible arsenical pump integral membrane protein arsB2 0.6069 0.029200206 mutA BCG_1555 Rv1492 Probable methylmalonyl-CoA mutase small subunit mutA 0.6052 0.012106302 menE BCG_0586c Rv0542c Possible o-succinylbenzoic acidCoA ligase menE 0.6049 0.01997206 BCG_3879 BCG_3879 Rv3817 Putative phosphotransferase 0.6039 0.027736949 BCG_1587 BCG_1587 Rv1535 Hypothetical...”
- Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.
Ruetz, Science (New York, N.Y.) 2019 - GeneRIF: study demonstrates itaconyl-CoA is a suicide inactivator of methylmalonyl-CoA mutase (MCM) ; crystallography and spectroscopy of the inhibited enzyme are consistent with a metal-centered cobalt radical ~6 angstroms away from the tertiary carbon-centered radical and suggest a means of controlling radical trajectories during MCM catalysis
- Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages
Flores-Valdez, Scientific reports 2024 - “...0.006884392 arsB2 BCG_3643 Rv3578 Possible arsenical pump integral membrane protein arsB2 0.6069 0.029200206 mutA BCG_1555 Rv1492 Probable methylmalonyl-CoA mutase small subunit mutA 0.6052 0.012106302 menE BCG_0586c Rv0542c Possible o-succinylbenzoic acidCoA ligase menE 0.6049 0.01997206 BCG_3879 BCG_3879 Rv3817 Putative phosphotransferase 0.6039 0.027736949 BCG_1587 BCG_1587 Rv1535 Hypothetical protein...”
- Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv
Sanoussi, Microbial genomics 2021 - “...in all six Illumina-sequenced genomes, and the one marked with a hash ( # ) (Rv1492), which is a gene present in all L5.3.2 strains and flanking the L5.3.2-specific deletion Gene name Size Co-ordinates in H37Rv Functional category Present in L5 Illumina-sequenced genomes % ( n...”
- Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B12
Mascarenhas, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret) - Propionate metabolism in a human pathogenic fungus: proteomic and biochemical analyses
Santos, IMA fungus 2020 - “...amino acid sequences of methylmalonyl-CoA mutases from C. elegans (accession number CAA84676) and M. tuberculosis (Rv1492 and Rv1493) (Savvi et al. 2008 ) shows no homologue in Paracoccidioides spp. Thus, it is unlikely that these fungi employ the methylmalonyl-CoA pathway in degradation of propionyl-CoA as previously...”
- More than cholesterol catabolism: regulatory vulnerabilities in Mycobacterium tuberculosis
Bonds, Current opinion in chemical biology 2018 - “...Cholesterol Side Chain Degradation -methyl-acyl-CoA racemase Rv1240 Mdh TCA Cycle & Glyoxylate Cycle Malate dehydrogenase Rv1492 MutA Methylmalonyl-CoA Pathway Methylmalonyl-CoA mutase (small subunit) Rv1493 MutB Methylmalonyl-CoA Pathway Methylmalonyl-CoA mutase (large subunit) Rv1837c GlcB Glyoxylate Cycle Malate synthase G Rv2215 DlaT Pyruvate Transformation Pyruvate dehydrogenase E2 component...”
- Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection
Zimmermann, mSystems 2017 - “...). This is further supported by the fact that the expression of mutA (methylmalonyl-CoA mutase, Rv1492), converting methylmalonyl-CoA to succinyl-CoA in the tricarboxylic acid (TCA) cycle, was downregulated ( Fig.5B ). These data underscore prior evidence of in vivo cholesterol consumption and indicate that the propanoyl-CoA...”
- Impact of Hypoxia on Drug Resistance and Growth Characteristics of Mycobacterium tuberculosis Clinical Isolates
Liu, PloS one 2016 - “...Rv1169c Lipase LipX Transcript regulation gene Pks3 Rv1180 Polyketide beta-ketoacyl synthase Transcript regulation gene MutA Rv1492 Methylmalonyl-CoA mutase small subunit Transcript regulation gene AccA3 Rv3285 Bifunctional protein acetyl-/propionyl-CoA carboxylase subunit alpha AccA Transcript regulation gene WhiB3 Rv3416 Redox-responsive transcriptional regulator WhiB3 Transcript regulation gene KstR Rv3574...”
- iniBAC induction Is Vitamin B12- and MutAB-dependent in Mycobacterium marinum
Boot, The Journal of biological chemistry 2016 - “...mshD H37Rv orthologue Gene length Rv3208 Rv2940c Rv2848 Rv1492 Rv1493 Rv1496 Rv2062c Rv2065 Rv2066 Rv2070c Rv2071c Rv2072c Rv0254c Rv2207 Rv2231c Rv2236c Rv1013...”
- More
PTH_1362 methylmalonyl-CoA mutase C-terminal domain-containing protein from Pelotomaculum thermopropionicum SI
46% identity, 18% coverage
ML1800 methylmalonyl-CoA mutase, [beta] subunit from Mycobacterium leprae TN
30% identity, 60% coverage
Q6TMA2 methylmalonyl-CoA mutase (EC 5.4.99.2) from Methylorubrum extorquens (see paper)
32% identity, 33% coverage
DEFDS_2077 methylmalonyl-CoA mutase C-terminal domain from Deferribacter desulfuricans SSM1
50% identity, 17% coverage
NJ7G_3672 cobalamin B12-binding domain-containing protein from Natrinema sp. J7-2
47% identity, 18% coverage
Q39VB8 (R)-methylmalonyl-CoA mutase, adenosylcobamide-binding subunit from Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)
47% identity, 18% coverage
Ngar_c24990 cobalamin B12-binding domain-containing protein from Candidatus Nitrososphaera gargensis Ga9.2
K0ILC3 Methylmalonyl-CoA mutase, small subunit from Nitrososphaera gargensis (strain Ga9.2)
42% identity, 19% coverage
A4YIE3 methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) from Metallosphaera sedula (see paper)
Msed_2055 cobalamin B12-binding domain protein from Metallosphaera sedula DSM 5348
43% identity, 18% coverage
- Enzymes Catalyzing Crotonyl-CoA Conversion to Acetoacetyl-CoA During the Autotrophic CO2 Fixation in Metallosphaera sedula
Liu, Frontiers in microbiology 2020 - “...Adams M. W. Kelly R. M. ( 2012 ). Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert ( S )-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle. Appl. Environ. Microbiol. 78 6194 6202 . 10.1128/AEM.01312-12 22752162 Hawkins A. B. Adams M. W. Kelly...”
- Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO2 fixation cycle in extremely thermoacidophilic archaea
Loder, Metabolic engineering 2016 - “...Han Y Hawkins AS Adams MW Kelly RM 2012 Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert ( S )-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle Appl Environ Microbiol 78 6194 202 22752162 Hansen T Urbanke C Leppanen VM Goldman A Brandenburg...”
- “...Methylmalonyl-CoA mutase MCM Msed_0638 ( R )-Methylmalonyl-CoA Succinyl-CoA R ( Marcheschi et al., 2012 ) Msed_2055 Succinic semialdehyde reductase (NADPH) SSR Msed_1424 Succinic semialdehyde + NADPH 4-Hydroxybutyrate + NADP R ( Kockelkorn and Fuchs, 2009 , this work) 4-Hydroxybutyryl-CoA synthetase (AMP-forming) HBCS Msed_0406 a) 4-Hydroxybutyrate +...”
- Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota
Leyn, Journal of bacteriology 2015 - “...Msed_1993 Msed_1456 Msed_1426 Msed_0639 Msed_0638 Msed_2055 Msed_1424 Msed_1422 Msed_1321 Msed_0656 Msed_1423 Msed_0363- Msed_0364 Msed_0743 ST2485 Msed_0773...”
- “...Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula...”
- Conversion of 4-hydroxybutyrate to acetyl coenzyme A and its anapleurosis in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway
Hawkins, Applied and environmental microbiology 2014 - “...Msed_0709 Msed_1993 Msed_1456 Msed_2001 Msed_1426 Msed_0639 Msed_0638, Msed_2055 Msed_1424 Msed_0406 Msed_1321 Msed_0399 Msed_0656 NCE (6, 34) R (35, 36) R (36)...”
- “...Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula...”
- Role of 4-hydroxybutyrate-CoA synthetase in the CO2 fixation cycle in thermoacidophilic archaea
Hawkins, The Journal of biological chemistry 2013 - “...Msed_1456 Msed_2001 Msed_1426 Msed_0639 Msed_0638 Msed_2055 Msed_1424 Msed_0394 Msed_0406 Msed_1321 Msed_0399 Msed_0656 CO2-H2 Autotrophy in Metallosphaera...”
- “...(Msed_ 0639) and mutase (Msed_0638, Msed_2055) convert (S)-methylmalonyl-CoA to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate...”
- Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle
Han, Applied and environmental microbiology 2012 - “...Msed_2055) Convert (S)-Methylmalonyl-Coenzyme A (CoA) to Succinyl-CoA in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Cycle Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North...”
- “...B12-binding subunit of MCM (MCM-) is located remotely (Msed_2055). The expression of all three genes was significantly upregulated under autotrophic compared to...”
- Novel B(12)-dependent acyl-CoA mutases and their biotechnological potential
Cracan, Biochemistry 2012 - “...16 Han Y Hawkins AS Adams MW Kelly RM Epimerase (Msed_ 0639) and Mutase (Msed_0638, Msed_2055) Convert (S)-Methylmalonyl-CoA to Succinyl-CoA in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Cycle App Environ Microbiol 2012 17 Menendez C Bauer Z Huber H Gad'on N Stetter KO Fuchs G Presence of acetyl...”
- “...used as examples: MCMs ( Propionibacterium shermanii ()(P11653, P11652), E. coli (2)(AAA69084), Metallosphaera sedula (22)(Msed_0638, Msed_2055) and Bacillus tusciae (22)(YP_003589181)); ICM ( Streptomyces cinnamonensis (22)(AAC08713, CAB59633)), IcmF ( Geobacillus kaustophilus (2)(YP_149244)), HCM ( Rhodobacter sphaeroides (22)(Rsph17029_3657, Rsph17029_3654)), and ECM ( Rhodobacter sphaeroides (2)(ACJ71670)). Figure 3 Active...”
- Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota
Ramos-Vera, Journal of bacteriology 2011 - “...encode MCMs in their genome (e.g., small subunit Msed_2055 and large subunit Msed_0638). Interestingly, Msed_2056 (ArgK-like) overlaps with the ORF encoding the...”
- More
WP_048060366 cobalamin B12-binding domain-containing protein from Metallosphaera prunae
43% identity, 18% coverage
SY28_RS02560 cobalamin B12-binding domain-containing protein from Meiothermus taiwanensis
47% identity, 18% coverage
Nmar_0958 cobalamin B12-binding domain protein from Nitrosopumilus maritimus SCM1
47% identity, 16% coverage
- Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production
Doxey, The ISME journal 2015 - “...as methionine synthase (Nmar_1267), ribonucleotide reductase (Nmar_1627), and methylmalonyl CoA mutase (B 12 binding domain, Nmar_0958), as well as probable cobalt transporters (Nmar_0878). As further support for cobalamin biosynthetic potential, we identified dual cob/cbi gene clusters conserved across all known ammonia-oxidizing thaumarchaeotal genomes. The two relevant...”
TON_1076 hypothetical methylmalony-CoA mutase from Thermococcus onnurineus NA1
40% identity, 18% coverage
PFJ30894_RS04420 cobalamin B12-binding domain-containing protein from Phascolarctobacterium faecium
48% identity, 15% coverage
rrnAC0934 putative methylmalonyl-CoA mutase from Haloarcula marismortui ATCC 43049
36% identity, 19% coverage
- Genome information management and integrated data analysis with HaloLex
Pfeiffer, Archives of microbiology 2008 - “...HQ1590A, OE2358F, NP3650A rrnAC0917 1,065 1,140 Shortened HQ1663A, OE1669F rrnAC0925 990 1,035 Shortened NP2796A, OE2451R rrnAC0934 423 471 Shortened NP2710A, OE2005F, HQ2301A rrnAC0942 1,611 1,416 Extended OE3436R rrnAC0944 1,302 1,350 Shortened HQ1663A, OE1669F rrnAC0956 462 537 Shortened HQ1497A, OE2934R rrnAC1042 1,806 1,851 Shortened rrnAC1570, HQ3533A rrnAC1083...”
O58013 methylmalonyl-CoA mutase (subunit 1/2) (EC 5.4.99.2) from Pyrococcus horikoshii (see paper)
PH0275 methylmalony-CoA mutase from Pyrococcus horikoshii OT3
40% identity, 18% coverage
WP_048053075 cobalamin-dependent protein from Pyrococcus horikoshii OT3
39% identity, 19% coverage
PFJ30894_RS01590 cobalamin B12-binding domain-containing protein from Phascolarctobacterium faecium
45% identity, 15% coverage
AF2219 methylmalonyl-CoA mutase, subunit alpha, C-terminus (mcmA2) from Archaeoglobus fulgidus DSM 4304
38% identity, 18% coverage
SCO4800 isobutiryl CoA mutase, small subunit from Streptomyces coelicolor A3(2)
42% identity, 18% coverage
icmB / Q9RJ84 isobutyryl-CoA mutase small subunit (EC 5.4.99.13) from Streptomyces virginiae (see 2 papers)
icmB / CAB59633.1 isobutyryl-CoA mutase, small subunit from Streptomyces cinnamonensis (see 2 papers)
46% identity, 15% coverage
NA23_RS08100 cobalamin B12-binding domain-containing protein from Fervidobacterium islandicum
42% identity, 17% coverage
- Functional Characterization of Primordial Protein Repair Enzyme M38 Metallo-Peptidase From Fervidobacterium islandicum AW-1
La, Frontiers in molecular biosciences 2020 - “...No use, distribution or reproduction is permitted which does not comply with these terms. The NA23_RS08100 gene of Fervidobacterium islandicum AW-1 encodes a keratin-degrading -aspartyl peptidase ( Fi BAP) that is highly expressed under starvation conditions. Herein, we expressed the gene in Escherichia coli , purified...”
- “...et al., 2005a ), which is more efficient at handling peptides containing isoAsp residues. The NA23_RS08100 gene encodes M38 -aspartyl peptidase (BAP) in the feather-degrading bacterium Fervidobacterium islandicum AW-1 (Nam et al., 2002 ; Lee et al., 2015a ). Among 57 genes encoding proteases in this...”
Mpe_B0538 methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) from Methylibium petroleiphilum PM1
43% identity, 15% coverage
X551_02556 cobalamin B12-binding domain-containing protein from Methylibium sp. T29
42% identity, 15% coverage
4r3uC / I3VE74 Crystal structure of 2-hydroxyisobutyryl-coa mutase (see paper)
43% identity, 15% coverage
- Ligand: cobalamin (4r3uC)
hcmB / I3VE74 2-hydroxyisobutanoyl-CoA mutase small subunit (EC 5.4.99.64) from Aquincola tertiaricarbonis (see 3 papers)
HCMB_AQUTE / I3VE74 2-hydroxyisobutanoyl-CoA mutase small subunit; 2-hydroxyisobutyryl-CoA mutase small subunit; HCM small subunit; EC 5.4.99.64 from Aquincola tertiaricarbonis (see 2 papers)
I3VE74 2-hydroxyisobutanoyl-CoA mutase (subunit 1/2) (EC 5.4.99.64) from Aquincola tertiaricarbonis (see 3 papers)
43% identity, 15% coverage
- function: Together with HcmA, catalyzes the isomerization of 2- hydroxyisobutyryl-CoA and 3-hydroxybutyryl-CoA. Is specific for 2- hydroxyisobutyryl-CoA and (S)-3-hydroxybutyryl-CoA, and shows only very low activity with (R)-3-hydroxybutyryl-CoA, isobutyryl-CoA and butyryl- CoA (PubMed:22433853, PubMed:25720495). In vitro, can isomerize pivalyl-CoA and isovaleryl-CoA, with much lower efficiency (PubMed:25720495). Plays a central role in the degradation of substrates bearing a tert-butyl moiety, such as the fuel oxygenate methyl tert-butyl ether (MTBE) and its metabolites (PubMed:22433853).
catalytic activity: 2-hydroxyisobutanoyl-CoA = (3S)-3-hydroxybutanoyl-CoA (RHEA:49592)
cofactor: adenosylcob(III)alamin
subunit: Homotetramer composed of two large substrate-binding subunits (HcmA) and two small cobalamin-binding subunits (HcmB).
disruption phenotype: Insertion mutant cannot grow on 2- hydroxyisobutyric acid (2-HIBA).
SCO6833 probable isobutyryl-CoA mutase, small subunit from Streptomyces coelicolor A3(2)
42% identity, 16% coverage
MUL_0366 methylmalonyl-CoA mutase alpha subunit, McmA2b from Mycobacterium ulcerans Agy99
41% identity, 17% coverage
CSP5_0925 cobalamin B12-binding domain-containing protein from Cuniculiplasma divulgatum
39% identity, 15% coverage
D5WTR8 2-hydroxyisobutanoyl-CoA mutase (subunit 1/2) (EC 5.4.99.64) from Kyrpidia tusciae DSM 2912 (see paper)
37% identity, 16% coverage
PCMB_XANP2 / A7IQE6 Pivalyl-CoA mutase small subunit; PCM small subunit; Pivalyl-CoA mutase, AdoCbl-binding subunit; EC 5.4.99.- from Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (see paper)
38% identity, 18% coverage
- function: Together with Xaut_5043, catalyzes the reversible isomerization between pivalyl-CoA and isovaleryl-CoA, using radical chemistry. Does not exhibit isobutyryl-CoA mutase (ICM) activity.
catalytic activity: 3-methylbutanoyl-CoA = 2,2-dimethylpropanoyl-CoA (RHEA:52620)
cofactor: adenosylcob(III)alamin
subunit: Monomer in the absence of the PCM large subunit. Weakly interacts with the PCM large subunit; an alpha(2)beta(2) stoichiometry seems to represent the active state of the enzyme.
MKAN_RS09965 cobalamin-dependent protein from Mycobacterium kansasii ATCC 12478
43% identity, 15% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...protein Rnase H/cobC cobF Precorrin-6A synthase MKAN_RS08645 A5717_31225 MXEN_19174 MSMEG_5548 cobA Probable cob(I)alamin adenosyltransferase CobO MKAN_RS09965 CDN37_RS24000 A5717_05685 MXEN_03569 AWC27_RS04140 cobB Cobyrinic acid A,C-diamide synthase A5717_05680 MXEN_03564 MSMEG_2617 cobC L-threonine 3-O-phosphate decarboxylase cobD Adenosylcobinamide-phosphate synthase MKAN_03275 A5717_01680 MXEN_00720 MSMEG_4310 cobG Precorrin-3B synthase MKAN_RS01775 CDN37_RS01855 MPHLCCUG_RS13200 A5717_31635...”
mgm / Q59268 α-methyleneglutarate mutase subunit (EC 5.4.99.4) from Eubacterium barkeri (see 4 papers)
MGM_EUBBA / Q59268 2-methyleneglutarate mutase; Alpha-methyleneglutarate mutase; EC 5.4.99.4 from Eubacterium barkeri (Clostridium barkeri) (see 7 papers)
31% identity, 18% coverage
- function: Involved in the fermentation of nicotinate to ammonia, propionate, acetate and carbon dioxide
catalytic activity: 2-methyleneglutarate = 2-methylene-3-methylsuccinate (RHEA:13793)
cofactor: adenosylcob(III)alamin cob(II)alamin (Contains a mixture of adenosylcobalamin and oxygen-stable cob(II)alamin.)
subunit: Homotetramer.
BACCAP_02289 hypothetical protein from Bacteroides capillosus ATCC 29799
30% identity, 18% coverage
- Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases
Li, Biotechnology for biofuels 2011 - “...[Geobacillus stearothermophilus] JF422024 H1 2-Methyleneglutarate mutase [Natranaerobius thermophilus JW/NM-WN-LF] 2-Methyleneglutarate mutase [Eubacterium barkeri] Hypothetical protein BACCAP_02289 [Bacteroides capillosus ATCC 29799] JF422029 B2 Beta-galactosidase [Clostridium hathewayi DSM 13479] Beta-glucosidase [Sorangium cellulosum 'So ce 56'] Beta-glucosidase [Acaryochloris marina MBIC11017] JF422027 D2 Beta-xylosidase, putative, xyl39A [Cellvibrio japonicus Ueda107] Candidate...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory