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PAFA_RHOJR
ID   PAFA_RHOJR              Reviewed;         452 AA.
AC   Q0SIG2;
DT   10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT   10-AUG-2010, sequence version 2.
DT   03-AUG-2022, entry version 96.
DE   RecName: Full=Pup--protein ligase {ECO:0000255|HAMAP-Rule:MF_02111};
DE            EC=6.3.1.19 {ECO:0000255|HAMAP-Rule:MF_02111};
DE   AltName: Full=Proteasome accessory factor A {ECO:0000255|HAMAP-Rule:MF_02111};
DE   AltName: Full=Pup-conjugating enzyme {ECO:0000255|HAMAP-Rule:MF_02111};
GN   Name=pafA {ECO:0000255|HAMAP-Rule:MF_02111};
GN   OrderedLocusNames=RHA1_ro00841;
OS   Rhodococcus jostii (strain RHA1).
OC   Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Rhodococcus.
OX   NCBI_TaxID=101510;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=RHA1;
RX   PubMed=17030794; DOI=10.1073/pnas.0607048103;
RA   McLeod M.P., Warren R.L., Hsiao W.W.L., Araki N., Myhre M., Fernandes C.,
RA   Miyazawa D., Wong W., Lillquist A.L., Wang D., Dosanjh M., Hara H.,
RA   Petrescu A., Morin R.D., Yang G., Stott J.M., Schein J.E., Shin H.,
RA   Smailus D., Siddiqui A.S., Marra M.A., Jones S.J.M., Holt R.,
RA   Brinkman F.S.L., Miyauchi K., Fukuda M., Davies J.E., Mohn W.W.,
RA   Eltis L.D.;
RT   "The complete genome of Rhodococcus sp. RHA1 provides insights into a
RT   catabolic powerhouse.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:15582-15587(2006).
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. {ECO:0000255|HAMAP-
CC       Rule:MF_02111}.
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:0000255|HAMAP-Rule:MF_02111};
CC   -!- PATHWAY: Protein degradation; proteasomal Pup-dependent pathway.
CC       {ECO:0000255|HAMAP-Rule:MF_02111}.
CC   -!- PATHWAY: Protein modification; protein pupylation. {ECO:0000255|HAMAP-
CC       Rule:MF_02111}.
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. {ECO:0000255|HAMAP-Rule:MF_02111}.
CC   -!- SIMILARITY: Belongs to the Pup ligase/Pup deamidase family. Pup-
CC       conjugating enzyme subfamily. {ECO:0000255|HAMAP-Rule:MF_02111}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ABG92674.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; CP000431; ABG92674.1; ALT_INIT; Genomic_DNA.
DR   AlphaFoldDB; Q0SIG2; -.
DR   SMR; Q0SIG2; -.
DR   STRING; 101510.RHA1_ro00841; -.
DR   EnsemblBacteria; ABG92674; ABG92674; RHA1_ro00841.
DR   KEGG; rha:RHA1_ro00841; -.
DR   eggNOG; COG0638; Bacteria.
DR   HOGENOM; CLU_040524_0_1_11; -.
DR   UniPathway; UPA00997; -.
DR   UniPathway; UPA00998; -.
DR   Proteomes; UP000008710; 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   Reference proteome; Ubl conjugation pathway.
FT   CHAIN           1..452
FT                   /note="Pup--protein ligase"
FT                   /id="PRO_0000395948"
FT   ACT_SITE        57
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         9
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         53
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         55
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         63
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         66
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         419
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
SQ   SEQUENCE   452 AA;  51232 MW;  9AFB3E416C4C60D4 CRC64;
     MQRRIMGIET EFGVTCTFHG HRRLSPDEVA RYLFRRVVSW GRSSNVFLRN GARLYLDVGS
     HPEYATAECD NLIQLVNHDR AGERVLEELL IDAEQRLAEE GIGGDIYLFK NNTDSAGNSY
     GCHENFLVAR AGEFSRISDV LLPFLVTRQL ICGAGKVLQT PKAATFCLSQ RAEHIWEGVS
     SATTRSRPII NTRDEPHADA EKYRRLHVIV GDSNMSESTT MLKVGTAALV LEMIEAGVSF
     RDFALDNPIR AIREVSHDVT GRRPVRLAGG RQASALDIQR EYHARAVEHL QNRDPDPQVT
     QVVDLWGRML DAVETQDFAK VDTEIDWVIK RKLFQRYQDR HGFELADPKI AQLDLAYHDI
     KRGRGVFDVL QRKGLVKRIT EDETIEAAVD TPPQTTRAKL RGEFITAAQE AGRDFTVDWV
     HLKLNDQAQR TVLCKDPFRS VDERVERLIA SM
 
 
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