PaperBLAST

Full List of Papers Linked to Q9WUM5

Q9WUM5 Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial from Mus musculus
NP_063932 succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial precursor from Mus musculus

• Neuronal SIRT3 Deletion Predisposes to Female-Specific Alterations in Cellular Metabolism, Memory, and Network Excitability
  Pearson-Smith, The Journal of neuroscience : the official journal of the Society for Neuroscience 2023 (secret)
• Treatment of microglia with Anti-PrP monoclonal antibodies induces neuronal apoptosis in vitro
  Adhikari, Heliyon 2021
  • “...cassette sub-family A member 8-A Abca8a Plasma membrane 2 60 0.00447174 12.7 Antibody Treatment Control Q9WUM5 Succinate--CoA ligase [ADP/GDP-forming] subunit alpha_ mitochondrial Suclg1 Mitochondrion 4 68.1 0.04593013 17.1 Antibody Treatment Control Q80XC6 Nuclear exosome regulator NRDE2 Nrde2 Nucleus 2 46.5 0.04874164 28.8 Antibody Treatment Control Q99JW2...”
• Identification of chronic brain protein changes and protein targets of serum auto-antibodies after blast-mediated traumatic brain injury
  Harper, Heliyon 2020
  • “...kDa 1 Q8C419 Gpr158 Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial IPI00406442 (+1) 36 kDa 1 Q9WUM5 Suclg1 LYR motif-containing protein 4 IPI00169804 11 kDa 1 Q8K215 Lyrm4 Phosphorylase b kinase regulatory subunit beta IPI00380735 124 kDa 1 Q7TSH2 Phkb Dihydropyrimidinase-related protein 2 IPI00114375 62 kDa 1...”
• PAX2 promotes epithelial ovarian cancer progression involving fatty acid metabolic reprogramming.
  Feng, International journal of oncology 2020
  • “...7 1.25 Up 0.0396 Tricarboxylic acid cycle Q9CZU6 Cs Citrate synthase, mitochondrial 1.14 - 0.1691 Q9WUM5 Suclg1 Succinyl-CoA ligase [ADP/GDP-forming] subunit , mitochondrial 1.55 Up 0.0112 Q8K2B3 Sdha Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial 1.23 Up 0.0374 P97807 Fh, Fh1 Fumarate hydratase, mitochondrial 1.21 - 0.0524...”
• Sirt3 regulates adipogenesis and adipokine secretion via its enzymatic activity.
  Ma, Pharmacology research & perspectives 2020
  • “...MICOS complex subunit Mic60 TSSVTLQTITAQNAAVQAVKAHSNILK 2.5 K256 Q05920 Pyruvate carboxylase LDNASAFQGAVISPHYDSLLVKVIAHGK 2.35 K428 TLHIKALAVSDLNR K1041 Q9WUM5 SuccinateCoA ligase [ADP/GDPforming] subunit alpha GGQKHLGLPVFNTVK 2.1 K94 Q60932 Voltagedependent anionselective channel protein 1 GYGFGLIKLDLK 2.1 K41 VNNSSLIGLGYTQTLKPGIK K265 Q03265 ATP synthase subunit alpha ITKFENAFLSHVISQHQSLLGNIR 1.85 K506 FNDGTDEKKK K241 HALIIYDDLSKQAVAYR...”
• The Effect of Neurotoxin MPTP and Neuroprotector Isatin on the Profile of Ubiquitinated Brain Mitochondrial Proteins
  Buneeva, Cells 2018
  • “...NACHT, LRR and PYD domains-containing protein 5 AT2A1_MOUSE Q8R429 Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 SUCA_MOUSE Q9WUM5 Succinate-CoA ligase (ADP/GDP-forming) subunit alpha, mitochondrial OAT_MOUSE P29758 Ornithine aminotransferase, mitochondrial MRP9_MOUSE Q80WJ6 Multidrug resistance-associated protein 9 DLDH_MOUSE O08749 Dihydrolipoyl dehydrogenase, mitochondrial CATB_MOUSE P10605 Cathepsin B CLH1_MOUSE Q68FD5 Clathrin heavy...”
  • “...K DPQEPIMK K437 95.86 Q9CZU4 * GTPase Era, mitochondrial Eral1 LNPQVLQCLT K FSQVPSILVLN K225 93.35 Q9WUM5 Succinate-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial Suclg1 KA K PVVSFIAGITAPPGR K280 100.00 P05202 Aspartate aminotransferase, mitochondrial Got2 GINVCLCQSYA K NMGLYGER K279 93.83 P47791 Glutathione reductase, mitochondrial Gsr RDAYVSRLNTIYQNNLT K K141...”
• Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.
  Vreven, Journal of molecular biology 2018
  • “...Q51567 -subunit P53593 1SCU (89%/77%) 1OI7 (58%) none 2.72 (3.95/n/a) Homology/Bound 2E Succinyl-CoA ligase -subunit Q9WUM5 -subunit Q9Z2I8 1EUC (94%/93%) 1OI7 (55%) none 1.14 (1.71/n/a) Homology/Bound 2F Succinyl-CoA ligase -subunit Q9WUM5 -subunit Q9Z2I9 1EUC (94%/55%) 1OI7 (55%) none 1.12 (1.69/n/a) Homology/Bound 3A F1-ATP synthase -subunit P06576...”
• Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction.
  López, BMC genomics 2018
  • “...the succinylation sites of specific proteins. These proteins included succinate-CoA ligase subunit alpha (UniProtKB ID Q9WUM5) whose absence causes severe disorders with antenatal manifestations [ 70 ], serine hydroxymethyltransferase (UniProtKB ID B1XB26) which regulates the metabolic partitioning of methylenetetrahydrofolate [ 71 ], and glutamate dehydrogenase 1...”
• Adenosine A1 receptor activation increases myocardial protein S-nitrosothiols and elicits protection from ischemia-reperfusion injury in male and female hearts
  Shao, PloS one 2017
  • “...flavoprotein, mitochondrial Q8K2B3 536 89, 536, 654 654 536, 654 536 654 Succinyl-CoA ligase alpha Q9WUM5 172, 181 172, 181 172, 181 172 60 172, 181 Succinyl-CoA ligase subunit beta, mitochondrial Q9Z2I9 430 152, 158, 270, 430 152, 158, 430 152, 158, 430 430 158, 430...”
• Localization and Processing of the Amyloid-β Protein Precursor in Mitochondria-Associated Membranes
  Del, Journal of Alzheimer's disease : JAD 2017
  • “...bound oxygenases Mitochondrial metabolism Q9JHI5 Isovaleryl-CoA dehydrogenase, mitochondrial GN=Ivd 1 Synthesis of (S)-3-hydroxy-3-methylglutaryl-CoA from 3-isovaleryl-CoA Q9WUM5 Succinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial GN=Suclg1 1 ATP- or GTP-dependent ligation of succinate and CoA to form succinyl-CoA Q9R112 Sulfide:quinone oxidoreductase, mitochondrial GN=Sqrdl 1 Oxidation of hydrogen sulfide with...”
• Proteomic Analysis of Mitochondria-Enriched Fraction Isolated from the Frontal Cortex and Hippocampus of Apolipoprotein E Knockout Mice Treated with Alda-1, an Activator of Mitochondrial Aldehyde Dehydrogenase (ALDH2).
  Stachowicz, International journal of molecular sciences 2017
  • “...light chain 1, cytoplasmic P63168 5 17 1.23 16 Succinyl-CoA ligase (ADP/GDP-forming) subunit , mitochondrial Q9WUM5 3 25 1.26 17 Ubiquitin-60S ribosomal protein L40 P62984 5 57 1.26 18 Cytochrome c oxidase subunit 7A2, mitochondrial P48771 2 7 1.33 19 Basigin P18572 2 4 1.41 20...”
• Characterization of the sex-dependent myocardial S-nitrosothiol proteome
  Shao, American journal of physiology. Heart and circulatory physiology 2016
  • “...(ND), 501 (ND), 502 (ND), 511 (ND), 591 (ND) Q8K2B3 Q9WUM5 Male HPAEC 127, 740 106, 212 357 445 Q8BH95 P63038 Male Male Male Ischemic postconditioning (Ref. 49)...”
• Polyamine transporter in Streptococcus pneumoniae is essential for evading early innate immune responses in pneumococcal pneumonia.
  Rai, Scientific reports 2016
  • “...1 P62874 3.3 SRSF1 serine/arginine-rich splicing factor 1 Q6PDM2 3.3 SUCLG1 succinate-CoA ligase, alpha subunit Q9WUM5 3.3 TGM2 transglutaminase 2 P21981 3.3 TNXB tenascin XB E9Q2T3 3.3 CAV1 caveolin 1, caveolae protein, 22kDa P49817 2.5 COL4A2 collagen, type IV, alpha 2 P08122 2.5 COL6A1 collagen, type...”
• RhoGDIβ Inhibits Bone Morphogenetic Protein 4 (BMP4)-induced Adipocyte Lineage Commitment and Favors Smooth Muscle-like Cell Differentiation.
  Huang, The Journal of biological chemistry 2015
• Quantitative proteomic analysis reveals metabolic alterations, calcium dysregulation, and increased expression of extracellular matrix proteins in laminin α2 chain-deficient muscle
  de, Molecular & cellular proteomics : MCP 2014
  • “...Q9JK37 Q6P8J7 Q60932 P06745 Q91YE8 A2ASS6 P63038 Q9CR68 Q9WUM5 Q9D855 P97457 P05977 P68134 P08249 Q61425 Q9CQC7 Q62234 Q06185 Q9Z1E4 P14152 Q9Z2I9 Q9D051 Q9D3D9...”
  • “...P97457 Q9Z2I9 P41216 Q6P8J7 P20801 Q9DCT2 P05977 Q91VD9 Q9WUM5 P48962 P05201 P28650 P62897 P05064 P11404 P54071 Q8BMS1 Q9CZU6 P08249 Q9QZ47 Q3TJD7 P12787 Q9CQ62...”
• Postconditioning leads to an increase in protein S-nitrosylation
  Tong, American journal of physiology. Heart and circulatory physiology 2014
  • “...Q91ZA3 Q9DBL1 Q9CZB0 Q8K2B3 Q8BWF0 Q9WUM5 Q9Z2I9 Voltage-dependent anion-selective channel-1 Voltage-dependent anion-selective channel-2* Voltage-dependent...”
• Transcriptome-wide profiling and posttranscriptional analysis of hematopoietic stem/progenitor cell differentiation toward myeloid commitment
  Klimmeck, Stem cell reports 2014
  • “...0.68 0.0629 0.63 0.0108 yes Q64105 ENSMUSG00000033735 Spr sepiapterin reductase 0.67 0.0762 0.87 0.0068 yes Q9WUM5 ENSMUSG00000052738 Suclg1 succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial 0.64 0.0855 0.33 0.0109 no Q9Z2I8 ENSMUSG00000061838 Suclg2 succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial 0.69 0.0617 0.57 0.0140 no Q93092 ENSMUSG00000025503 Taldo1...”
• Proteomic analysis of the SH2 domain-containing leukocyte protein of 76 kDa (SLP76) interactome in resting and activated primary mast cells [corrected]
  Bounab, Molecular & cellular proteomics : MCP 2013
  • “...Cytoskeleton regulation Adapter Protein Phospholipase P98083 Q9QZK7 Q3UND0 Q9WUM5 GRB2 SKAP1 HECD3 MSH2 CSTF1 FYB BTK PACS1 1433 1433 Q99M59 CLNK VAV Linker for...”
• Cyclophilin D modulates mitochondrial acetylome.
  Nguyen, Circulation research 2013
  • “...5 KCRS_MOUSE (Q6P8J7) Creatine kinase S-type YYALSEMTEQDQQR 0.950 0.116 0.480 0.018 0.505 0.02 6 SUCA_MOUSE (Q9WUM5) Succinyl-CoA ligase [GDP-forming] subunit alpha NT k IIcQGFTGK 0.853 0.073 0.530 0.048 0.621 0.02 HLGLPVFNTVAEAK 0.829 0.092 0.564 0.012 0.681 0.05 7 THIL_MOUSE (Q8QZT1) Acetyl-CoA acetyltransferase VL k YAGLK 0.955...”
• Regulation of protein function and signaling by reversible cysteine S-nitrosylation.
  Gould, The Journal of biological chemistry 2013
• Uterine deletion of Trp53 compromises antioxidant responses in the mouse decidua.
  Burnum, Endocrinology 2012
• Radiation-induced signaling results in mitochondrial impairment in mouse heart at 4 weeks after exposure to X-rays
  Barjaktarovic, PloS one 2011
  • “...3;5;1 0.611 8.0 O35143 ATPIF1 12.2 9.64 ATPase inhibitor, mitochondrial 34.91 3 2;5;2 0.632 2.2 Q9WUM5 SUCLG1 35.0 9.39 Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial 10.51 2 4;3;3 0.661 2.0 Q8BK30 NDUFV3 50.5 8.97 NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial 20.09 4 2;2;- 0.668 7.7 Q62425...”
• Simultaneous measurement of protein oxidation and S-nitrosylation during preconditioning and ischemia/reperfusion injury with resin-assisted capture.
  Kohr, Circulation research 2011
  • “...22.40 * 53 0.30 * , 54 9.91 * , , 58 Succinyl-CoA ligase (M) Q9WUM5 II C QGFTGK 60 1 40 0.71 48 0.23 * , 43 0.63 45 Triosephosphate isomerase P17751 IAVAAQN C YK 67 1 59 3.40 * 62 0.44 * , 53...”
• iTRAQ analysis of complex proteome alterations in 3xTgAD Alzheimer's mice: understanding the interface between physiology and disease.
  Martin, PloS one 2008
  • “...Bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830086I04 product:heat shock protein 8 1.4 SUCA_MOUSE (Q9WUM5) Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial precursor (EC 6.2.1.4) 1.4 TBB5_MOUSE (P99024) Tubulin beta-5 chain 1.43 DNM1L_MOUSE (Q8K1M6) Dynamin-1-like protein (EC 3.6.5.5) (Dynamin-related protein 1) (Dynamin family member proline-rich) 1.5 PAK1_MOUSE...”
• SUCLG1 restricts POLRMT succinylation to enhance mitochondrial biogenesis and leukemia progression.
  Yan, The EMBO journal 2024
  • GeneRIF: SUCLG1 restricts POLRMT succinylation to enhance mitochondrial biogenesis and leukemia progression.
• Expression of two succinyl-CoA synthetases with different nucleotide specificities in mammalian tissues.
  Lambeth, The Journal of biological chemistry 2004 (PubMed)
  • GeneRIF: ADP and GDP succinyl-CoA synthetases have different expression patterns and specificity

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How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.