PAFA_ACIFD
ID PAFA_ACIFD Reviewed; 455 AA.
AC C7LYP9;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 13-OCT-2009, sequence version 1.
DT 03-AUG-2022, entry version 63.
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=Afer_0912;
OS Acidimicrobium ferrooxidans (strain DSM 10331 / JCM 15462 / NBRC 103882 /
OS ICP).
OC Bacteria; Actinobacteria; Acidimicrobiia; Acidimicrobiales;
OC Acidimicrobiaceae; Acidimicrobium.
OX NCBI_TaxID=525909;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10331 / JCM 15462 / NBRC 103882 / ICP;
RX PubMed=21304635; DOI=10.4056/sigs.1463;
RA Clum A., Nolan M., Lang E., Glavina Del Rio T., Tice H., Copeland A.,
RA Cheng J.F., Lucas S., Chen F., Bruce D., Goodwin L., Pitluck S.,
RA Ivanova N., Mavrommatis K., Mikhailova N., Pati A., Chen A.,
RA Palaniappan K., Goker M., Spring S., Land M., Hauser L., Chang Y.J.,
RA Jeffries C.C., Chain P., Bristow J., Eisen J.A., Markowitz V.,
RA Hugenholtz P., Kyrpides N.C., Klenk H.P., Lapidus A.;
RT "Complete genome sequence of Acidimicrobium ferrooxidans type strain
RT (ICP).";
RL Stand. Genomic Sci. 1:38-45(2009).
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; CP001631; ACU53857.1; -; Genomic_DNA.
DR AlphaFoldDB; C7LYP9; -.
DR SMR; C7LYP9; -.
DR STRING; 525909.Afer_0912; -.
DR EnsemblBacteria; ACU53857; ACU53857; Afer_0912.
DR KEGG; afo:Afer_0912; -.
DR eggNOG; COG0638; Bacteria.
DR HOGENOM; CLU_040524_0_1_11; -.
DR OMA; CVSQRAE; -.
DR UniPathway; UPA00997; -.
DR UniPathway; UPA00998; -.
DR Proteomes; UP000000771; 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..455
FT /note="Pup--protein ligase"
FT /id="PRO_0000395889"
FT ACT_SITE 60
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 12
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 56
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 58
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 66
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 69
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT BINDING 422
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
SQ SEQUENCE 455 AA; 52008 MW; 2999BF29B32FEAF6 CRC64;
MPRLARRIYG IENEYGITCT QRGQRRLSPD EVARYLFRRV VSWGRSSNVF LENGARLYLD
VGSHPEYATP ECDSLSDLVA HDKAGERILE SLAHSAEAKM REEGIRGDVF LLKNNTDSAG
NSYGCHENYL TVRVDDLTRL VEVLIPFLVS RQIIAGAGKV LLTSRGPLYA VSQRAEHIWE
GVSSATTRSR PIINTRDEPH ADAERYRRLH VIVGDSNMSQ WATYLKVGAM AIVLRLLEEE
VVLRDLTLEN PIRAIREIAH DTELERTVRL VNGRELTGLE IQEAYFERAE RYHERIGLPA
DEARALDMWR EALKALRAND HEALFGKVDW VTKLTLIEAF RARHQLPLSH PQVSLLDLQY
HDISRERGLF ARLEAKGRVP RIVDDETIER AVDEPPATTR AALRGRFIRA AKEAHRDYTV
DWVHLKLNDQ AQRTVMLKDP FASEDERVDR LLTSI
