PAFA_KINRD
ID PAFA_KINRD Reviewed; 453 AA.
AC A6W972;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 21-AUG-2007, sequence version 1.
DT 03-AUG-2022, entry version 73.
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=Krad_1875;
OS Kineococcus radiotolerans (strain ATCC BAA-149 / DSM 14245 / SRS30216).
OC Bacteria; Actinobacteria; Kineosporiales; Kineosporiaceae; Kineococcus.
OX NCBI_TaxID=266940;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-149 / DSM 14245 / SRS30216;
RX PubMed=19057647; DOI=10.1371/journal.pone.0003878;
RA Bagwell C.E., Bhat S., Hawkins G.M., Smith B.W., Biswas T., Hoover T.R.,
RA Saunders E., Han C.S., Tsodikov O.V., Shimkets L.J.;
RT "Survival in nuclear waste, extreme resistance, and potential applications
RT gleaned from the genome sequence of Kineococcus radiotolerans SRS30216.";
RL PLoS ONE 3:e3878-e3878(2008).
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}.
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DR EMBL; CP000750; ABS03361.1; -; Genomic_DNA.
DR RefSeq; WP_011981500.1; NC_009664.2.
DR AlphaFoldDB; A6W972; -.
DR SMR; A6W972; -.
DR STRING; 266940.Krad_1875; -.
DR MEROPS; U72.001; -.
DR EnsemblBacteria; ABS03361; ABS03361; Krad_1875.
DR KEGG; kra:Krad_1875; -.
DR eggNOG; COG0638; Bacteria.
DR HOGENOM; CLU_040524_0_1_11; -.
DR OMA; CVSQRAE; -.
DR OrthoDB; 537546at2; -.
DR UniPathway; UPA00997; -.
DR UniPathway; UPA00998; -.
DR Proteomes; UP000001116; 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..453
FT /note="Pup--protein ligase"
FT /id="PRO_0000395919"
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 420
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
SQ SEQUENCE 453 AA; 51774 MW; F05EB1DAC91512DA CRC64;
MDRRIFGLET EFGVTCAFEG QRKLSPDEVA RYLFRKVVSW GRSSNVFLKN GARLYLDVGS
HPEYATPECD DVRQLVVHDR AGERTLEGLL TDAERRLEEE GIAGEVFLFK NNTDSAGNSY
GCHENYLVSR HGEFGKLSDV LIPFLVSRQL IVGAGKVVQT PRGAVYSLSQ RADHIWEGVS
SATTRSRPII NTRDEPHADA ERYRRLHVIV GDSNMSETTT MLKLGATDLV LRMVEEGVVL
REMTMENPIR AIREISHDMT GRKPVRLANG REASALEIQE EYLEKAKEFV ESRGLQTPTI
KRVLDLWERA LRAVATQDFS LVDREVDWVI KKKLLDRYMA KHDLPLTSPR IARLDLAYHD
IHRKRGLHYM LAERGMAERV CSDIEVFEAL SVPPQTTRAK LRGDFVRAAQ EKRRDFTVDW
VHLKLNDQAQ RTVLCKDPFK AVDDRVERLI DSM
