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PAFA_STRRD
ID   PAFA_STRRD              Reviewed;         452 AA.
AC   D2ATU8;
DT   10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT   09-FEB-2010, sequence version 1.
DT   03-AUG-2022, entry version 65.
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=Sros_5868;
OS   Streptosporangium roseum (strain ATCC 12428 / DSM 43021 / JCM 3005 / NI
OS   9100).
OC   Bacteria; Actinobacteria; Streptosporangiales; Streptosporangiaceae;
OC   Streptosporangium.
OX   NCBI_TaxID=479432;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 12428 / DSM 43021 / JCM 3005 / NI 9100;
RX   PubMed=21304675; DOI=10.4056/sigs.631049;
RA   Nolan M., Sikorski J., Jando M., Lucas S., Lapidus A., Glavina Del Rio T.,
RA   Chen F., Tice H., Pitluck S., Cheng J.F., Chertkov O., Sims D., Meincke L.,
RA   Brettin T., Han C., Detter J.C., Bruce D., Goodwin L., Land M., Hauser L.,
RA   Chang Y.J., Jeffries C.D., Ivanova N., Mavromatis K., Mikhailova N.,
RA   Chen A., Palaniappan K., Chain P., Rohde M., Goker M., Bristow J.,
RA   Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.;
RT   "Complete genome sequence of Streptosporangium roseum type strain (NI
RT   9100).";
RL   Stand. Genomic Sci. 2:29-37(2010).
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; CP001814; ACZ88603.1; -; Genomic_DNA.
DR   RefSeq; WP_012892338.1; NC_013595.1.
DR   AlphaFoldDB; D2ATU8; -.
DR   SMR; D2ATU8; -.
DR   STRING; 479432.Sros_5868; -.
DR   MEROPS; U72.001; -.
DR   EnsemblBacteria; ACZ88603; ACZ88603; Sros_5868.
DR   KEGG; sro:Sros_5868; -.
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; UP000002029; 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_0000395959"
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;  51890 MW;  B8AE5677E41F224E CRC64;
     MDRRIFGLEN EYGVTCTFRG QRRLSPDEVA RYLFRRVVSW GRSSNVFLRN GARLYLDVGS
     HPEYATPECD NVVELVTHDK AGERILEGLL VDAEKRLREE GIAGDIYLFK NNTDSAGNSY
     GCHENYLVGR HGEFGRLADV LIPFLVTRQI VCGAGKVLQT PRGAVYCVSQ RAEHIWEGVS
     SATTRSRPII NTRDEPHADA ERFRRLHVIV GDSNMSETTM LLKVGATDLV LRMIEAGTVM
     RDLSLENPIR AIREVSHDMT GRRRVRLANG REASSLEIQQ EYLSKARDFV DRRGGDEISH
     RVLELWERTL NAVETGNLDL VAREIDWVTK YQLIERYRKK YDLPLSSPRV AQLDLAYHDV
     HRRRGLFYLL QKRGAVERVA SDLKIFEAKS VPPQTTRARL RGEFIRKAQE KRRDFTVDWV
     HLKLNDQAQR TVLCKDPFRS VDERVDKLIA GM
 
 
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