PAFA_CORDI
ID PAFA_CORDI Reviewed; 479 AA.
AC Q6NH95;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 83.
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}; OrderedLocusNames=DIP1245;
OS Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype
OS gravis).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=257309;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700971 / NCTC 13129 / Biotype gravis;
RX PubMed=14602910; DOI=10.1093/nar/gkg874;
RA Cerdeno-Tarraga A.-M., Efstratiou A., Dover L.G., Holden M.T.G.,
RA Pallen M.J., Bentley S.D., Besra G.S., Churcher C.M., James K.D.,
RA De Zoysa A., Chillingworth T., Cronin A., Dowd L., Feltwell T., Hamlin N.,
RA Holroyd S., Jagels K., Moule S., Quail M.A., Rabbinowitsch E.,
RA Rutherford K.M., Thomson N.R., Unwin L., Whitehead S., Barrell B.G.,
RA Parkhill J.;
RT "The complete genome sequence and analysis of Corynebacterium diphtheriae
RT NCTC13129.";
RL Nucleic Acids Res. 31:6516-6523(2003).
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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BX248357; CAE49774.1; -; Genomic_DNA.
DR AlphaFoldDB; Q6NH95; -.
DR SMR; Q6NH95; -.
DR STRING; 257309.DIP1245; -.
DR PRIDE; Q6NH95; -.
DR EnsemblBacteria; CAE49774; CAE49774; DIP1245.
DR KEGG; cdi:DIP1245; -.
DR HOGENOM; CLU_040524_0_1_11; -.
DR OMA; CVSQRAE; -.
DR UniPathway; UPA00997; -.
DR UniPathway; UPA00998; -.
DR Proteomes; UP000002198; 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..479
FT /note="Pup--protein ligase"
FT /id="PRO_0000395906"
FT ACT_SITE 66
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 17
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 62
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 64
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 72
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 75
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 432
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
SQ SEQUENCE 479 AA; 53460 MW; 4EDE74739B2868D2 CRC64;
MGEYERTVFT RRITGVETEY GITCVGDNSR RRLGADEAAR YMFRPVVEEW GSSNVFIPNG
ARLYLDVGSH PEYASAECDS LSQLIAYDRA GDKIVDQLAQ RAETALATEG IGGRVYLFKN
NLDSLGNSYG CHENYLVSRD VVLKTLGRQL LPFLITRQLI CGAGSIQDGQ FQVSQRADHV
WEGVSSATTR SRPIINTRDE PHADSHRFRR LHVIVGDSNM SETTCALKIG STQLVLEMIE
AGALSHDLEL SNEIAAIREI SRDITGMAPV PLKAGTSMPA IEIQRRYAEK ALCWLEQRGD
TEGTPNAEMH KVVSLWLDTI SAIESNDLQA LSRDIDWAIK LSLLRRAQRR IGCSESDFTH
PKLAQLDLAY HDIRAGRGVF PVLESKQLVN RWINDTDIEQ ATRIAPSTTR AALRGEFLTA
AKKLQAPISA DWLRLKVNRP EPQIIELTDP FENTDDRVDQ LISYMRNHAA SYSTDTAIS
