ID   PAFA_MYCTO              Reviewed;         452 AA.
AC   P9WNU6; 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 37.
DE   RecName: Full=Pup--protein ligase;
DE            EC=6.3.1.19;
DE   AltName: Full=Proteasome accessory factor A;
DE   AltName: Full=Pup-conjugating enzyme;
GN   Name=pafA; Synonyms=paf; OrderedLocusNames=MT2158;
OS   Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycobacterium; Mycobacterium tuberculosis complex.
OX   NCBI_TaxID=83331;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CDC 1551 / Oshkosh;
RX   PubMed=12218036; DOI=10.1128/jb.184.19.5479-5490.2002;
RA   Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O.,
RA   Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K.,
RA   Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L.,
RA   Delcher A., Utterback T.R., Weidman J.F., Khouri H.M., Gill J., Mikula A.,
RA   Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M.;
RT   "Whole-genome comparison of Mycobacterium tuberculosis clinical and
RT   laboratory strains.";
RL   J. Bacteriol. 184:5479-5490(2002).
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:0000250}.
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   -!- 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:0000250}.
CC   -!- SIMILARITY: Belongs to the Pup ligase/Pup deamidase family. Pup-
CC       conjugating enzyme subfamily. {ECO:0000305}.
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DR   EMBL; AE000516; AAK46439.1; -; Genomic_DNA.
DR   PIR; D70768; D70768.
DR   RefSeq; WP_003410781.1; NZ_KK341227.1.
DR   AlphaFoldDB; P9WNU6; -.
DR   SMR; P9WNU6; -.
DR   EnsemblBacteria; AAK46439; AAK46439; MT2158.
DR   GeneID; 45426074; -.
DR   KEGG; mtc:MT2158; -.
DR   PATRIC; fig|83331.31.peg.2327; -.
DR   HOGENOM; CLU_040524_0_1_11; -.
DR   UniPathway; UPA00997; -.
DR   UniPathway; UPA00998; -.
DR   Proteomes; UP000001020; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016879; F:ligase activity, forming carbon-nitrogen bonds; IEA:InterPro.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0019787; F:ubiquitin-like protein transferase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0019941; P:modification-dependent protein catabolic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0010498; P:proteasomal protein catabolic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0070490; P:protein pupylation; IEA:UniProtKB-UniRule.
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   3: Inferred from homology;
KW   ATP-binding; Ligase; Magnesium; Metal-binding; Nucleotide-binding;
KW   Ubl conjugation pathway; Virulence.
FT   CHAIN           1..452
FT                   /note="Pup--protein ligase"
FT                   /id="PRO_0000427065"
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"
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