PAFA_SACVD
ID PAFA_SACVD Reviewed; 452 AA.
AC C7MWV3;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 13-OCT-2009, sequence version 1.
DT 03-AUG-2022, entry version 66.
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=Svir_21990;
OS Saccharomonospora viridis (strain ATCC 15386 / DSM 43017 / JCM 3036 / NBRC
OS 12207 / P101).
OC Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
OC Saccharomonospora.
OX NCBI_TaxID=471857;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15386 / DSM 43017 / JCM 3036 / NBRC 12207 / P101;
RX PubMed=21304650; DOI=10.4056/sigs.20263;
RA Pati A., Sikorski J., Nolan M., Lapidus A., Copeland A.,
RA Glavina Del Rio T., Lucas S., Chen F., Tice H., Pitluck S., Cheng J.F.,
RA Chertkov O., Brettin T., Han C., Detter J.C., Kuske C., Bruce D.,
RA Goodwin L., Chain P., D'haeseleer P., Chen A., Palaniappan K., Ivanova N.,
RA Mavromatis K., Mikhailova N., Rohde M., Tindall B.J., Goker M., Bristow J.,
RA Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT "Complete genome sequence of Saccharomonospora viridis type strain
RT (P101).";
RL Stand. Genomic Sci. 1:141-149(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}.
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DR EMBL; CP001683; ACU97207.1; -; Genomic_DNA.
DR RefSeq; WP_015786520.1; NC_013159.1.
DR AlphaFoldDB; C7MWV3; -.
DR SMR; C7MWV3; -.
DR STRING; 471857.Svir_21990; -.
DR MEROPS; U72.001; -.
DR EnsemblBacteria; ACU97207; ACU97207; Svir_21990.
DR KEGG; svi:Svir_21990; -.
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; UP000000841; 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_0000395950"
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; 51296 MW; 546CCEDEC34B34F1 CRC64;
MQRRIFGIET EFGVTCTFHG QRRLSPDEVA RYLFRRVVSW GRSSNVFLSN GSRLYLDVGS
HPEYATAECD DLAQLVTHDK AGERILEDLL IDAERRLAEE GIGGDIFLFK NNTDSAGNSY
GCHENYLVTR AGEFSRVADV LLPFLVTRQL VCGAGKVLQT PRGGVYCLSQ RAEHIWEGVS
SATTRSRPII NTRDEPHADA ERYRRLHVIV GDSNMAEPTT LLKVGSVHLV LQMIEEGVQF
RDFTLDNPIR AIREISHDLT GRRQVRLAGG REASALEIQR EYYARAVQHV ESGDPSPTTQ
YLIDLWGRAL DAVEQQDFSS IDTEIDWAIK HRLVERYRSK HNLTLSDPRV AQLDLAYHDI
RRGRGVFDLL QRKGMVRRIT DDGEIELAKD SPPQTTRAKL RGDFIAAAQE AGRDFTVDWV
HLKLNDQAQR TVLCKDPFRS VDERVERLIN SL
