PAFA_MYCTU
ID PAFA_MYCTU Reviewed; 452 AA.
AC P9WNU7; A0A111; L0T8N5; P64943; Q10706;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 40.
DE RecName: Full=Pup--protein ligase;
DE EC=6.3.1.19 {ECO:0000269|PubMed:19448618, ECO:0000269|PubMed:20355727};
DE AltName: Full=Proteasome accessory factor A;
DE AltName: Full=Pup-conjugating enzyme;
GN Name=pafA; Synonyms=paf; OrderedLocusNames=Rv2097c; ORFNames=MTCY49.37c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=17277063; DOI=10.1128/jb.01597-06;
RA Festa R.A., Pearce M.J., Darwin K.H.;
RT "Characterization of the proteasome accessory factor (paf) operon in
RT Mycobacterium tuberculosis.";
RL J. Bacteriol. 189:3044-3050(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [3]
RP ROLE IN RESISTANCE TO RNI, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=14671303; DOI=10.1126/science.1091176;
RA Darwin K.H., Ehrt S., Gutierrez-Ramos J.-C., Weich N., Nathan C.F.;
RT "The proteasome of Mycobacterium tuberculosis is required for resistance to
RT nitric oxide.";
RL Science 302:1963-1966(2003).
RN [4]
RP FUNCTION IN THE PROTEASOME DEGRADATION PATHWAY.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=17082771; DOI=10.1038/sj.emboj.7601405;
RA Pearce M.J., Arora P., Festa R.A., Butler-Wu S.M., Gokhale R.S.,
RA Darwin K.H.;
RT "Identification of substrates of the Mycobacterium tuberculosis
RT proteasome.";
RL EMBO J. 25:5423-5432(2006).
RN [5]
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=18832610; DOI=10.1126/science.1163885;
RA Pearce M.J., Mintseris J., Ferreyra J., Gygi S.P., Darwin K.H.;
RT "Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium
RT tuberculosis.";
RL Science 322:1104-1107(2008).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH PUP, REACTION MECHANISM, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=19448618; DOI=10.1038/nsmb.1597;
RA Striebel F., Imkamp F., Sutter M., Steiner M., Mamedov A., Weber-Ban E.;
RT "Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to
RT substrates by distinct but homologous enzymes.";
RL Nat. Struct. Mol. Biol. 16:647-651(2009).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND LIGATION REACTION.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=20355727; DOI=10.1021/ja910546x;
RA Sutter M., Damberger F.F., Imkamp F., Allain F.H., Weber-Ban E.;
RT "Prokaryotic ubiquitin-like protein (Pup) is coupled to substrates via the
RT side chain of its C-terminal glutamate.";
RL J. Am. Chem. Soc. 132:5610-5612(2010).
RN [8]
RP MUTAGENESIS OF GLU-9; GLU-11; ARG-53; TYR-55; ASP-57; GLU-63; HIS-123;
RP ARG-171; ARG-187 AND HIS-207.
RX PubMed=20636328; DOI=10.1111/j.1365-2958.2010.07276.x;
RA Cerda-Maira F.A., Pearce M.J., Fuortes M., Bishai W.R., Hubbard S.R.,
RA Darwin K.H.;
RT "Molecular analysis of the prokaryotic ubiquitin-like protein (Pup)
RT conjugation pathway in Mycobacterium tuberculosis.";
RL Mol. Microbiol. 77:1123-1135(2010).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
CC -!- FUNCTION: Catalyzes the covalent attachment of the prokaryotic
CC ubiquitin-like protein modifier Pup to the proteasomal substrate
CC proteins, thereby targeting them for proteasomal degradation. This
CC tagging system is termed pupylation. The ligation reaction involves the
CC side-chain carboxylate of the C-terminal glutamate of Pup and the side-
CC chain amino group of a substrate lysine. PafA is required to confer
CC resistance against the lethal effects of reactive nitrogen
CC intermediates (RNI), antimicrobial molecules produced by activated
CC macrophages and other cell types. {ECO:0000269|PubMed:14671303,
CC ECO:0000269|PubMed:17082771, ECO:0000269|PubMed:19448618,
CC ECO:0000269|PubMed:20355727}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + [prokaryotic ubiquitin-like protein]-L-glutamate +
CC [protein]-L-lysine = ADP + phosphate + N(6)-([prokaryotic ubiquitin-
CC like protein]-gamma-L-glutamyl)-[protein]-L-lysine.; EC=6.3.1.19;
CC Evidence={ECO:0000269|PubMed:19448618, ECO:0000269|PubMed:20355727};
CC -!- PATHWAY: Protein degradation; proteasomal Pup-dependent pathway.
CC -!- PATHWAY: Protein modification; protein pupylation.
CC -!- SUBUNIT: Interacts with the prokaryotic ubiquitin-like protein Pup.
CC {ECO:0000269|PubMed:19448618}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene have no detectable
CC pupylated proteins and substrate proteins accumulate. These cells also
CC become hypersensitive to reactive nitrogen intermediates (RNI) and fail
CC to grow in both wild-type and nitric oxide synthase 2 deficient
CC macrophages. Moreover, they display increased resistance to hydrogen
CC peroxide. {ECO:0000269|PubMed:14671303, ECO:0000269|PubMed:18832610}.
CC -!- MISCELLANEOUS: The reaction mechanism probably proceeds via the
CC activation of Pup by phosphorylation of its C-terminal glutamate, which
CC is then subject to nucleophilic attack by the substrate lysine,
CC resulting in an isopeptide bond and the release of phosphate as a good
CC leaving group.
CC -!- SIMILARITY: Belongs to the Pup ligase/Pup deamidase family. Pup-
CC conjugating enzyme subfamily. {ECO:0000305}.
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DR EMBL; DQ990836; ABJ90140.1; -; Genomic_DNA.
DR EMBL; AL123456; CCP44872.1; -; Genomic_DNA.
DR PIR; D70768; D70768.
DR RefSeq; NP_216613.1; NC_000962.3.
DR RefSeq; WP_003410781.1; NZ_KK339370.1.
DR AlphaFoldDB; P9WNU7; -.
DR SMR; P9WNU7; -.
DR STRING; 83332.Rv2097c; -.
DR PaxDb; P9WNU7; -.
DR DNASU; 888460; -.
DR GeneID; 45426074; -.
DR GeneID; 888460; -.
DR KEGG; mtu:Rv2097c; -.
DR PATRIC; fig|83332.111.peg.2337; -.
DR TubercuList; Rv2097c; -.
DR eggNOG; COG0638; Bacteria.
DR OMA; CVSQRAE; -.
DR PhylomeDB; P9WNU7; -.
DR BioCyc; MetaCyc:G185E-6303-MON; -.
DR BRENDA; 6.3.1.19; 3445.
DR UniPathway; UPA00997; -.
DR UniPathway; UPA00998; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0016881; F:acid-amino acid ligase activity; IDA:MTBBASE.
DR GO; GO:0005524; F:ATP binding; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019787; F:ubiquitin-like protein transferase activity; IDA:UniProtKB.
DR GO; GO:0071732; P:cellular response to nitric oxide; IMP:UniProtKB.
DR GO; GO:0030682; P:mitigation of host defenses by symbiont; IMP:UniProtKB.
DR GO; GO:0019941; P:modification-dependent protein catabolic process; IMP:UniProtKB.
DR GO; GO:0010498; P:proteasomal protein catabolic process; IMP:UniProtKB.
DR GO; GO:0070490; P:protein pupylation; IDA:UniProtKB.
DR GO; GO:0051409; P:response to nitrosative stress; IMP:MTBBASE.
DR HAMAP; MF_02111; Pup_ligase; 1.
DR InterPro; IPR022279; Pup_ligase.
DR InterPro; IPR004347; Pup_ligase/deamidase.
DR PANTHER; PTHR42307; PTHR42307; 1.
DR Pfam; PF03136; Pup_ligase; 1.
DR PIRSF; PIRSF018077; UCP018077; 1.
DR TIGRFAMs; TIGR03686; pupylate_PafA; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Ligase; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome; Ubl conjugation pathway; Virulence.
FT CHAIN 1..452
FT /note="Pup--protein ligase"
FT /id="PRO_0000103966"
FT ACT_SITE 57
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 53
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 55
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 63
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 66
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 419
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MUTAGEN 9
FT /note="E->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 11
FT /note="E->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 53
FT /note="R->E: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 55
FT /note="Y->K: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 57
FT /note="D->N: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 63
FT /note="E->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 123
FT /note="H->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 171
FT /note="R->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 187
FT /note="R->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
FT MUTAGEN 207
FT /note="H->E: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:20636328"
SQ SEQUENCE 452 AA; 51384 MW; 12AF8B7872D2F5EA CRC64;
MQRRIMGIET EFGVTCTFHG HRRLSPDEVA RYLFRRVVSW GRSSNVFLRN GARLYLDVGS
HPEYATAECD SLVQLVTHDR AGEWVLEDLL VDAEQRLADE GIGGDIYLFK NNTDSAGNSY
GCHENYLIVR AGEFSRISDV LLPFLVTRQL ICGAGKVLQT PKAATYCLSQ RAEHIWEGVS
SATTRSRPII NTRDEPHADA EKYRRLHVIV GDSNMSETTT MLKVGTAALV LEMIESGVAF
RDFSLDNPIR AIREVSHDVT GRRPVRLAGG RQASALDIQR EYYTRAVEHL QTREPNAQIE
QVVDLWGRQL DAVESQDFAK VDTEIDWVIK RKLFQRYQDR YDMELSHPKI AQLDLAYHDI
KRGRGIFDLL QRKGLAARVT TDEEIAEAVD QPPQTTRARL RGEFISAAQE AGRDFTVDWV
HLKLNDQAQR TVLCKDPFRA VDERVKRLIA SM
