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PAFA_JONDD
ID   PAFA_JONDD              Reviewed;         459 AA.
AC   C7R405;
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=Jden_1206;
OS   Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / BCRC 15368 / CIP
OS   55.134 / JCM 11481 / NBRC 15587 / NCTC 10816 / Prevot 55134) (Listeria
OS   denitrificans).
OC   Bacteria; Actinobacteria; Micrococcales; Jonesiaceae; Jonesia.
OX   NCBI_TaxID=471856;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 14870 / DSM 20603 / BCRC 15368 / CIP 55.134 / JCM 11481 / NBRC
RC   15587 / NCTC 10816 / Prevot 55134;
RX   PubMed=21304666; DOI=10.4056/sigs.41646;
RA   Pukall R., Gehrich-Schroter G., Lapidus A., Nolan M., Glavina Del Rio T.,
RA   Lucas S., Chen F., Tice H., Pitluck S., Cheng J.F., Copeland A.,
RA   Saunders E., Brettin T., Detter J.C., Bruce D., Goodwin L., Pati A.,
RA   Ivanova N., Mavromatis K., Ovchinnikova G., Chen A., Palaniappan K.,
RA   Land M., Hauser L., Chang Y.J., Jeffries C.D., Chain P., Goker M.,
RA   Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C.,
RA   Klenk H.P., Han C.;
RT   "Complete genome sequence of Jonesia denitrificans type strain (Prevot
RT   55134).";
RL   Stand. Genomic Sci. 1:262-269(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; CP001706; ACV08862.1; -; Genomic_DNA.
DR   RefSeq; WP_015771490.1; NC_013174.1.
DR   AlphaFoldDB; C7R405; -.
DR   SMR; C7R405; -.
DR   STRING; 471856.Jden_1206; -.
DR   MEROPS; U72.001; -.
DR   EnsemblBacteria; ACV08862; ACV08862; Jden_1206.
DR   KEGG; jde:Jden_1206; -.
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; UP000000628; 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..459
FT                   /note="Pup--protein ligase"
FT                   /id="PRO_0000395918"
FT   ACT_SITE        58
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         54
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         56
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
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         67
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
FT   BINDING         421
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
SQ   SEQUENCE   459 AA;  51770 MW;  A1BCE74D48BF958C CRC64;
     MTRRIFGLET EYGITYAHPT DDVTLSADEV ARQLFKKVVA WGRSSNVFLR NGSRLYLDVG
     SHPEYATAEC DSVEQLIAHD RGGELILVDL IDDAQRRLAQ EGYTGTIHLL KNNTDSAGNS
     YGCHENYLVR RQGDFTRLAD ILIPFLITRQ VVVGAGKIMS TPQGPRYCFS QRADHMWEAV
     SSATTRSRPI INTRDEPHAD AEFYRRLHVI VGDSNIAEPT TFLKVGATDM VLRLIEAGVP
     MRDLALDNAM RAIREISHDI TGRATVTLSS GKTVTAWQLQ EMYVEKVRTY VESLGPLSPT
     DEAVFELWER ALRAVETQDH SLIDRDIDWA IKKRLLDRTQ DRLGCALDDP RLARLDLAYH
     DISPATGLGH RLVSRSMMNR VVSDAEVERA SQVAPETTRA HLRGRFVTAA QEQKKDYTVD
     WVHLKLNDQA QRTVLCKDPF AHVDDRVDQL IDSMRTQAT
 
 
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