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PAFA_CATAD
ID   PAFA_CATAD              Reviewed;         453 AA.
AC   C7PVV4;
DT   10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT   13-OCT-2009, sequence version 1.
DT   03-AUG-2022, entry version 68.
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=Caci_2428;
OS   Catenulispora acidiphila (strain DSM 44928 / JCM 14897 / NBRC 102108 / NRRL
OS   B-24433 / ID139908).
OC   Bacteria; Actinobacteria; Catenulisporales; Catenulisporaceae;
OC   Catenulispora.
OX   NCBI_TaxID=479433;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 44928 / JCM 14897 / NBRC 102108 / NRRL B-24433 / ID139908;
RX   PubMed=21304647; DOI=10.4056/sigs.17259;
RA   Copeland A., Lapidus A., Glavina Del Rio T., Nolan M., Lucas S., Chen F.,
RA   Tice H., Cheng J.F., Bruce D., Goodwin L., Pitluck S., Mikhailova N.,
RA   Pati A., Ivanova N., Mavromatis K., Chen A., Palaniappan K., Chain P.,
RA   Land M., Hauser L., Chang Y.J., Jeffries C.D., Chertkov O., Brettin T.,
RA   Detter J.C., Han C., Ali Z., 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 Catenulispora acidiphila type strain (ID
RT   139908).";
RL   Stand. Genomic Sci. 1:119-125(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; CP001700; ACU71346.1; -; Genomic_DNA.
DR   RefSeq; WP_012786639.1; NC_013131.1.
DR   AlphaFoldDB; C7PVV4; -.
DR   SMR; C7PVV4; -.
DR   STRING; 479433.Caci_2428; -.
DR   MEROPS; U72.001; -.
DR   EnsemblBacteria; ACU71346; ACU71346; Caci_2428.
DR   KEGG; cai:Caci_2428; -.
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; UP000000851; 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_0000395904"
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;  51890 MW;  E4A9651A37B191CF CRC64;
     MDRRIFGLEN EYGVTCTFRG QRRLSPDEVA RYLFRRVVSW GRSSNVFLRN GARLYLDVGS
     HPEYATPECD SVRELIVHDK AGERILEGLL ADAERRLHEE GIAGDVYLFK NNTDSAGNSY
     GCHENYLVGR HGEFSRLADV LIPFLVTRQL ICGAGKVLAT PRGAVYCVSQ RAEHIWEGVS
     SATTRSRPII NTRDEPHADA EKYRRLHVIV GDSNMSETTM LLKVGATDLV LRMIEAGTTL
     RDMTLENPIR AIREVSHDMT GQKKVRLANG REMSALEIQE EYFTKARDFA EKRGLRTGAV
     DRILDLWERT LTAVNTGDLD LISREIDWVI KYQLIERYRA KNNLAMSAPR VAQLDLAYHD
     ISRNRGLYYL LEKRGMVERT ATDLEIFQAK SVPPQTTRAR LRGEFIKRAQ EQRRDFTVDW
     VHLKLNDQAQ RTVLCKDPFR SVDERVEKLI SSM
 
 
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