ID PAFA_ACTMD Reviewed; 452 AA. AC C6WIE4; DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot. DT 22-SEP-2009, sequence version 1. DT 27-MAR-2024, entry version 76. 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}; GN OrderedLocusNames=Amir_2247; OS Actinosynnema mirum (strain ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 OS / NCIMB 13271 / NRRL B-12336 / IMRU 3971 / 101). OC Bacteria; Actinomycetota; Actinomycetes; Pseudonocardiales; OC Pseudonocardiaceae; Actinosynnema. OX NCBI_TaxID=446462; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 29888 / DSM 43827 / JCM 3225 / NBRC 14064 / NCIMB 13271 / RC NRRL B-12336 / IMRU 3971 / 101; RX PubMed=21304636; DOI=10.4056/sigs.21137; RA Land M., Lapidus A., Mayilraj S., Chen F., Copeland A., Del Rio T.G., RA Nolan M., Lucas S., Tice H., Cheng J.F., Chertkov O., Bruce D., Goodwin L., RA Pitluck S., Rohde M., Goker M., Pati A., Ivanova N., Mavromatis K., RA Chen A., Palaniappan K., Hauser L., Chang Y.J., Jeffries C.C., Brettin T., RA Detter J.C., Han C., Chain P., Tindall B.J., Bristow J., Eisen J.A., RA Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P.; RT "Complete genome sequence of Actinosynnema mirum type strain (101)."; RL Stand. Genomic Sci. 1:46-53(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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; CP001630; ACU36187.1; -; Genomic_DNA. DR RefSeq; WP_015801076.1; NC_013093.1. DR AlphaFoldDB; C6WIE4; -. DR SMR; C6WIE4; -. DR STRING; 446462.Amir_2247; -. DR MEROPS; U72.001; -. DR KEGG; ami:Amir_2247; -. DR eggNOG; COG0638; Bacteria. DR HOGENOM; CLU_040524_0_1_11; -. DR OrthoDB; 9760627at2; -. DR UniPathway; UPA00997; -. DR UniPathway; UPA00998; -. DR Proteomes; UP000002213; 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 NCBIfam; TIGR03686; pupylate_PafA; 1. DR PANTHER; PTHR42307; PUP DEAMIDASE/DEPUPYLASE; 1. DR PANTHER; PTHR42307:SF3; PUP--PROTEIN LIGASE; 1. DR Pfam; PF03136; Pup_ligase; 1. DR PIRSF; PIRSF018077; UCP018077; 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_0000395891" 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; 51144 MW; B3D3D861D86BCC59 CRC64; MQRRIFGIET EFGVTCTFHG QRRLSPDEVA RYLFRRVVSW GRSSNVFLRN GSRLYLDVGS HPEYATAECD DLAQLVSHDK AGERILEDLL VDAERRLADE GIGGDIFLFK NNTDSAGNSY GCHENYLVAR AGEFSRIADV LLPFLVTRQL ICGAGKVLQT PRGAVYCLSQ RAEHIWEGVS SATTRSRPII NTRDEPHADA ERYRRLHVIV GDSNMSEVTT LLKVGSANLV LEMIEQGVQF RDFSLDNPIR AIREISHDLT GRRTVKLAGG KEASALDIQR EYYERAVEHV AKRSPDPMAE RVLELWGRTL DAIAAQDLSK IDREIDWAIK HRLLERYQAK HDMDLSNPRI AQLDLAYHDI RRGRGVFDLL QRKGQVERVT DDGEIEAAKD TPPQTTRAKL RGDFIAAAQA AGRDFTVDWV HLKLNDQAQR TVLCKDPFRA VDERVERLIA SL //