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PAFA_BRAFD
ID   PAFA_BRAFD              Reviewed;         473 AA.
AC   C7MCY7;
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=Bfae_16170;
OS   Brachybacterium faecium (strain ATCC 43885 / DSM 4810 / JCM 11609 / LMG
OS   19847 / NBRC 14762 / NCIMB 9860 / 6-10).
OC   Bacteria; Actinobacteria; Micrococcales; Dermabacteraceae; Brachybacterium.
OX   NCBI_TaxID=446465;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43885 / DSM 4810 / JCM 11609 / LMG 19847 / NBRC 14762 / NCIMB
RC   9860 / 6-10;
RX   PubMed=21304631; DOI=10.4056/sigs.492;
RA   Lapidus A., Pukall R., Labuttii K., Copeland A., Del Rio T.G., Nolan M.,
RA   Chen F., Lucas S., Tice H., Cheng J.F., Bruce D., Goodwin L., Pitluck S.,
RA   Rohde M., Goker M., Pati A., Ivanova N., Mavrommatis K., Chen A.,
RA   Palaniappan K., D'haeseleer P., Chain P., Bristow J., Eisen J.A.,
RA   Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT   "Complete genome sequence of Brachybacterium faecium type strain
RT   (Schefferle 6-10).";
RL   Stand. Genomic Sci. 1:3-11(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; CP001643; ACU85444.1; -; Genomic_DNA.
DR   RefSeq; WP_012805215.1; NC_013172.1.
DR   RefSeq; YP_003155034.1; NC_013172.1.
DR   AlphaFoldDB; C7MCY7; -.
DR   SMR; C7MCY7; -.
DR   STRING; 446465.Bfae_16170; -.
DR   MEROPS; U72.001; -.
DR   EnsemblBacteria; ACU85444; ACU85444; Bfae_16170.
DR   KEGG; bfa:Bfae_16170; -.
DR   PATRIC; fig|446465.5.peg.1610; -.
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; UP000001919; 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   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..473
FT                   /note="Pup--protein ligase"
FT                   /id="PRO_0000395903"
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         425
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_02111"
SQ   SEQUENCE   473 AA;  52118 MW;  A5DE9BB67E92F192 CRC64;
     MKRRVGGLET EYGLVCVRAD GSRALEPEAA ARELFRPVVA MGRSSNVFLR NAARLYLDVG
     SHPEYATAEC DDWWELVAQD RAGDRMFAEL AAEATERLAA DGQDARIHLL KNNVDSAGNA
     FGSHENYLVD RRGEFTRLPR YLLPFLVTRQ IVTGAGGVVR PAPADGAPEQ EAGPAQFVFS
     RRSDHMWEAV SSATTRTRPI INTRDEPHGD PTRFRRLHVI VGDSTMSEVS THLRFATTDL
     VLRAIESGRA LPELALHDDI AAIRAVARDL TGTTAIPTAD GGTTTAIEVQ QRWLDHVTEF
     ADESEQDVLE TWQRGIDAVR TGDRSWAATH LDWAIKERLF HQVAERRGVD LGDPAIERLD
     LAYHDIDPTQ SVFAALQRRG LAPQVLDEQR IERARTTAPT TTRAHLRGQV VTAAQEHGVD
     HVVDWTTLRL TRPGAMPVQV LDPFATELPA VDALLEEIRA SAAGAPESPP PFA
 
 
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