Family Search for PF10021 (PARG_cat_microb)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

PF10021 hits 12 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

SCO0909 hypothetical protein from Streptomyces coelicolor A3(2)
Aligns to 59:199 / 329 (42.9%), covers 100.0% of PF10021, 180.3 bits

• Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA
  Hloušek-Kasun, Computational and structural biotechnology journal 2022
  • “...DraG/ARH homologues (SCO0086, SCO1766, SCO2028, SCO2029, SCO2030, SCO2031, SCO4435, SCO5809) and three are macrodomain hydrolases SCO0909 (bacterial-type PARG), SCO6450 (MacroD homologue) and SCO6735 (ALC1-like). Both SCO6450 and SCO6735 can remove mono-ADP-ribosylation from protein substrates [30] , [17] . Furthermore, SCO6450 can remove mono-ADP-ribosylation from phosphorylated 5-RNA...”
• The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition
  Lee, mBio 2020
  • “...SCO4388 (D). (E and F) Examples of antisense RNAs originated from UTRs of the neighboring SCO0909 (E) and SCO1988 (F) genes. Download FIGS2, PDF file, 0.4 MB . Copyright 2020 Lee et al. 2020 Lee et al. This content is distributed under the terms of the...”
• ADP-ribosylation: new facets of an ancient modification
  Palazzo, The FEBS journal 2017
  • “...process in Streptomycescoelicolor ADPribosyltransferases SCO2860 (Arr homologue) SCO3953 (Tpt1/KptA homologue) SCO5461 (Pierisin homologue) Macrodomain hydrolases SCO0909 (bacterialtype PARG) SCO6450 (MacroD homologue) SCO6735 (TARG1like) DraG/ARH like hydrolases SCO0086 SCO1766 SCO2028 SCO2029 SCO2030 SCO2031 SCO4435 SCO5809 Sirtuins SCO0452 SCO6464 John Wiley & Sons, Ltd This article is being...”
  • “...are macrodomain proteins representing three different classes within the macrodomain superfamily (Table 1 ). The SCO0909 is a bacterialtype PARG that cleaves the PARylation in the same manner as mammalian PARGs 36 . Nothing is known about the function of SCO0909, but in the radiationresistant bacterium...”
• Disruption of Macrodomain Protein SCO6735 Increases Antibiotic Production in Streptomyces coelicolor
  Lalić, The Journal of biological chemistry 2016 (no snippet)

3sigA / D1AC29 The x-ray crystal structure of poly(adp-ribose) glycohydrolase (parg) bound to adp-ribose from thermomonospora curvata (see paper)
Aligns to 8:149 / 265 (53.6%), covers 100.0% of PF10021, 179.4 bits

• Ligand: [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl[hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (3sigA)

D1AC29 poly(ADP-ribose) glycohydrolase (EC 3.2.1.143) from Thermomonospora curvata (see paper)
Tcur_1721 hypothetical protein from Thermomonospora curvata DSM 43183
Aligns to 47:197 / 316 (47.8%), covers 100.0% of PF10021, 179.4 bits

• The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase
  Slade, Nature 2011
  • “...PARG gene (Q86W56) were amplified from HeLa cDNA, while the T. curvata DSM 43183 gene (Tcur_1721 ) and the A. variabilis ATCC 29413 gene (Ava_4013) were synthesised according to the database sequence (GenScript USA Inc.). The H. aurantiacus ATCC 23779 PARG (Haur_1618) and PARP (Haur_4763) genes...”

alr1372 hypothetical protein from Nostoc sp. PCC 7120
Aligns to 7:159 / 278 (55.0%), covers 100.0% of PF10021, 172.7 bits

• Global translational control by the transcriptional repressor TrcR in the filamentous cyanobacterium Anabaena sp. PCC 7120
  Wang, Communications biology 2023
  • “...endonuclease; Restriction endonuclease alr0739 71.56269 hypothetical protein alr0740 42.48551 slipin family protein; membrane protease subunit alr1372 12.89042 TIGR02452 family protein alr1537 50.08121 GNAT family N-acetyltransferase alr1538 38.23092 DMT family transporter alr1539 23.77193 cupin domain-containing protein alr1540 6.225956 N-acetylmuramoyl-L-alanine amidase alr1554 112.6749 ABC transporter ATP-binding protein alr3301...”
• Group 3 sigma factor gene, sigJ, a key regulator of desiccation tolerance, regulates the synthesis of extracellular polysaccharide in cyanobacterium Anabaena sp. strain PCC 7120
  Yoshimura, DNA research : an international journal for rapid publication of reports on genes and genomes 2007
  • “...to NifU protein 2.77 0.81 alr1016 Hypothetical protein 2.41 2.01 alr1183 Unknown protein 2.76 1.30 alr1372 Hypothetical protein 2.27 1.56 alr1534 Hypothetical protein 2.09 0.80 alr2071 Unknown protein 2.13 2.03 alr2142 Oxidoreductase 2.09 1.36 alr2174 Transcriptional regulator 2.10 0.38 alr2256 Unknown protein 2.95 1.51 alr2310 Similar...”

Haur_1618 hypothetical protein from Herpetosiphon aurantiacus ATCC 23779
Aligns to 10:154 / 271 (53.5%), covers 99.3% of PF10021, 169.2 bits

• Comparative inhibitory profile and distribution of bacterial PARPs, using Clostridioides difficile CD160 PARP as a model
  García-Saura, Scientific reports 2018
  • “...DNA from Herpetosiphon aurantiacus DSM785, purchased from DSMZ (Braunschweig, Germany), was used to clone PARG (Haur_1618) and PARP (Haur_4763) genes. hPARG-pCMV6-XL5 construct was purchased from Origene (Rockville, USA). Genes were amplified by PCR using KAPA HiFi DNA polymerase and the corresponding primers, including Nhe I and...”
• The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase
  Slade, Nature 2011
  • “...synthesised according to the database sequence (GenScript USA Inc.). The H. aurantiacus ATCC 23779 PARG (Haur_1618) and PARP (Haur_4763) genes were amplified from genomic DNA extracted from a dried culture purchased from DSMZ. All proteins bear an N-terminal his tag with the exception of the A....”

SNA_17125 TIGR02452 family protein from Streptomyces natalensis ATCC 27448
Aligns to 9:162 / 295 (52.2%), covers 100.0% of PF10021, 167.2 bits

• Streptomyces natalensis programmed cell death and morphological differentiation are dependent on oxidative stress
  Beites, Scientific reports 2015
  • “...Absent Unknown function SNA_01165 (17) Hypothetical protein Up ( * ) Up ( * ) SNA_17125 (36) superfamily DUF2263 Up ( # 3.8) Up (5.6) SNA_27255 (23) Hypothetical protein Down ( # 0.7) Down (0.4) Proteins were grouped according to the functional categorization available for S....”

Q9RZM4 poly(ADP-ribose) glycohydrolase (EC 3.2.1.143) from Deinococcus radiodurans (see paper)
DRB0099 hypothetical protein from Deinococcus radiodurans R1
DR_B0099 TIGR02452 family protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Aligns to 10:159 / 285 (52.6%), covers 100.0% of PF10021, 152.6 bits

• Structure/function studies of the NAD⁺-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding
  Fernandes, Extremophiles : life under extreme conditions 2023
  • “...who demonstrated that DrLigB possesses DNA end-joining activity but requires other deinococcal proteins, namely PprA (DrB0099) and protein DrB0098 for its function. On the contrary, DrLigA possesses DNA ligation activity with different DNA substrates, requiring only the cofactor NAD + and divalent metals to be active...”
• ATP-type DNA ligase requires other proteins for its activity in vitro and its operon components for radiation resistance in Deinococcus radiodurans in vivo
  Kota, Biochemistry and cell biology = Biochimie et biologie cellulaire 2010 (PubMed)
  • “...copy of drB0100 along with other genes such as drb0099 and drb0098, organized downstream in the operon. The in vitro DNA ligase activity of LigB was stimulated...”
  • “...did not improve when PprA was substituted with purified DRB0099 protein or when DRB0098 protein was substituted with the DRB0099 protein in the presence of PprA...”
• [Construction of the gene drb0099 deleted mutant and adversity analysis in the extremely radioresistant bacterium Deinococcus radiodurans]
  Chang, Wei sheng wu xue bao = Acta microbiologica Sinica 2008 (PubMed)
  • “...Deinococcus radiodurans R1 has extraordinary resistance to radiation. DRB0099 might play an important role in protecting the bacterium against radiation. To verify the inference, we deleted drb0099 and constructed the mutant. Comparing with the wild type, the mutant grew...”
  • “...lower with UV treatment time increased, the survival fraction was much higher than that of drb0099. The wild type could repair DNA double strands breaks better than the mutant. The gene drb0099 might directly relate with the DNA repair system. The mutant was more sensitive to...”
• Enzymes involved in DNA ligation and end-healing in the radioresistant bacterium Deinococcus radiodurans
  Blasius, BMC molecular biology 2007
  • “...addition, DRB0100 belongs to a putative DNA repair operon together with the genes DRB0098 and DRB0099. DRB0098 has been predicted to encode a kinase/phosphatase with an unusual domain architecture [ 9 ] whereas DRB0099 is classified as a domain of unknown function with weak similarity to...”
  • “...and a polynucleotide kinase domain and resembles the human repair protein PNKP [ 27 ]; DRB0099 is an open reading frame with unknown function and weak similarity to macro domains [ 8 , 10 ]. No DNA ligation was detected with any of these three operon...”
• Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance
  Omelchenko, BMC evolutionary biology 2005
  • “...DRB0098, a protein containing an HD family phosphatase and polynucleotide kinase domains [ 7 ]; DRB0099, a predicted phosphatase of the H2Macro superfamily ([ 27 ] and KSM, unpublished observations); a double-stranded DNA-binding protein PprA (DRA0346), which stimulates the DNA end-joining reaction in vitro [ 77...”
• Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species
  Lim, FEMS microbiology reviews 2019
  • “...2 1 1 1 1 1 1 1 1 DR_B0100 1 1 1 1 1 DR_B0099 1 1 DR_B0098 1 1 1 1 1 DR_B0094 1 1 1 DR_B0095 fr 1 Other DNA repair proteins TopA 1 1 1 2 3 2 2 1 1 1...”
  • “...(Liu etal. 2003 ). DR_B0100 is the first gene of a radiation-induced operon also encoding DR_B0099 (poly ADP-ribose glycohydrolase) and DR_B0098 (polynucleotide kinase) (Blasius etal. 2007 ; Slade etal. 2011 ). A DR_B0100 mutant is IR resistant as the wild type according to one study (Makarova...”
• N ⁴-Cytosine DNA Methylation Is Involved in the Maintenance of Genomic Stability in Deinococcus radiodurans
  Li, Frontiers in microbiology 2019
  • “...2.42E-26 DNA damage repair protein, PprA DNA repair proteins DR_1262 7.4276 1.96E-155 Ribonucleoprotein Ro/SS-A-like protein DR_B0099 3.3137 5.88E-18 Poly ADP-ribose glycohydrolase, PARG DR_1297 3.09 6.24E-12 Uncharacterized membrane protein, MutK DR_0221 2.7957 1.35E-07 Endonuclease domain-containing protein (DUF559) DR_0596 2.6105 2.51E-14 DNA helicase subunit, RuvB DR_1902 2.6449 2.96E-11...”
• Deletion of the rnl gene encoding a nick-sealing RNA ligase sensitizes Deinococcus radiodurans to ionizing radiation
  Schmier, Nucleic acids research 2017
  • “...8 ). LigB is encoded by the first ORF in a three-gene operon that includes DR_B0099 , a poly ADP-ribose glycohydrolase ( 9 ), and DR_B0098 , a 5-OH polynucleotide kinase ( 7 ). This operon is transcriptionally upregulated at 1.5 to 12 h after exposure...”
• The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase
  Slade, Nature 2011
  • “...pColdTF vector (Takara). The A. fumigatus Af293 gene (AFUA_4G11940), the D. radiodurans R1 ATCC13939 gene (DR_B0099) and the E. dispar SAW760 gene (EDI_110590) were amplified from genomic DNA, the human PARP1 and PARG gene (Q86W56) were amplified from HeLa cDNA, while the T. curvata DSM 43183...”

5zdbA / Q9RZM4 Crystal structure of poly(adp-ribose) glycohydrolase (parg) from deinococcus radiodurans in complex with adp-ribose (p21) (see paper)
Aligns to 2:131 / 253 (51.4%), covers 82.2% of PF10021, 144.4 bits

• Ligand: [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl[hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (5zdbA)

AFUA_2G02500 conserved hypothetical protein from Aspergillus fumigatus Af293
Aligns to 17:143 / 271 (46.9%), covers 78.1% of PF10021, 79.4 bits

• RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
  Irmer, BMC genomics 2015
  • “...U3 small nucleolar ribonucleoprotein protein 2.23 AFUA_3G06380 exosome-associated family protein 2.24 AFUA_4G14180 hypothetical protein 2.25 AFUA_2G02500 hypothetical protein 2.26 1.60 AFUA_5G04010 tRNA-splicing endonuclease subunit Sen2 2.32 AFUA_2G02970 hypothetical protein 2.34 AFUA_6G03750 amidophosphoribosyltransferase 2.38 AFUA_8G01850 phosphate-repressible phosphate permease 2.43 AFUA_8G05720 DUF567 domain protein 2.44 AFUA_4G14190 hypothetical protein...”

AFUA_4G11940 conserved hypothetical protein from Aspergillus fumigatus Af293
Aligns to 13:201 / 335 (56.4%), covers 69.9% of PF10021, 71.6 bits

• The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase
  Slade, Nature 2011
  • “...N-terminal truncation (1-455) was expressed from the pColdTF vector (Takara). The A. fumigatus Af293 gene (AFUA_4G11940), the D. radiodurans R1 ATCC13939 gene (DR_B0099) and the E. dispar SAW760 gene (EDI_110590) were amplified from genomic DNA, the human PARP1 and PARG gene (Q86W56) were amplified from HeLa...”

K0N7J8 Microbial-type PARG catalytic domain-containing protein from Lacticaseibacillus paracasei
Aligns to 4:137 / 252 (53.2%), covers 77.4% of PF10021, 71.4 bits

• Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress
  Adu, PloS one 2018
  • “...fabD K0NBT1 BN194_22570 + + + - Malonyl CoA-acyl carrier protein, Transacylase fatty acid biosynthesis K0N7J8 BN194_23650 + + + - Amino acid-related metabolism Unknown dnaX K0MXD3 BN194_23990 + + + - DNA polymerase III subunit gamma/tau DNA replication, elongation K0N7R2 BN194_24650 + + + -...”

BN194_23650 TIGR02452 family protein from Lacticaseibacillus paracasei
Aligns to 2:132 / 247 (53.0%), covers 76.7% of PF10021, 71.2 bits

• Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress
  Adu, PloS one 2018
  • “...K0NBT1 BN194_22570 + + + - Malonyl CoA-acyl carrier protein, Transacylase fatty acid biosynthesis K0N7J8 BN194_23650 + + + - Amino acid-related metabolism Unknown dnaX K0MXD3 BN194_23990 + + + - DNA polymerase III subunit gamma/tau DNA replication, elongation K0N7R2 BN194_24650 + + + - YjdJ...”

Or search for genetic data about PF10021 in the Fitness Browser