PAFA_CORGL
ID PAFA_CORGL Reviewed; 482 AA.
AC Q8NQE1; Q6M590;
DT 10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 2.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=Pup--protein ligase {ECO:0000255|HAMAP-Rule:MF_02111};
DE EC=6.3.1.19 {ECO:0000255|HAMAP-Rule:MF_02111, ECO:0000269|PubMed:22910360};
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=Cgl1494, cg1688;
OS Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 /
OS JCM 1318 / LMG 3730 / NCIMB 10025).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=196627;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12743753; DOI=10.1007/s00253-003-1328-1;
RA Ikeda M., Nakagawa S.;
RT "The Corynebacterium glutamicum genome: features and impacts on
RT biotechnological processes.";
RL Appl. Microbiol. Biotechnol. 62:99-109(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12948626; DOI=10.1016/s0168-1656(03)00154-8;
RA Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A.,
RA Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A.,
RA Hartmann M., Huthmacher K., Kraemer R., Linke B., McHardy A.C., Meyer F.,
RA Moeckel B., Pfefferle W., Puehler A., Rey D.A., Rueckert C., Rupp O.,
RA Sahm H., Wendisch V.F., Wiegraebe I., Tauch A.;
RT "The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its
RT impact on the production of L-aspartate-derived amino acids and vitamins.";
RL J. Biotechnol. 104:5-25(2003).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.16 ANGSTROMS) IN COMPLEX WITH ADP, FUNCTION,
RP CATALYTIC ACTIVITY, ACTIVE SITE, AND MUTAGENESIS OF GLU-16; GLU-18; ARG-60;
RP ASP-64; HIS-68; HIS-130; ARG-199; ARG-201; HIS-211; HIS-221; LEU-376 AND
RP TRP-440.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=22910360; DOI=10.1038/ncomms2009;
RA Ozcelik D., Barandun J., Schmitz N., Sutter M., Guth E., Damberger F.F.,
RA Allain F.H., Ban N., Weber-Ban E.;
RT "Structures of Pup ligase PafA and depupylase Dop from the prokaryotic
RT ubiquitin-like modification pathway.";
RL Nat. Commun. 3:1014-1014(2012).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH PROTEIN PUP; ATP AND
RP MAGNESIUM, INTERACTION WITH PUP, AND MUTAGENESIS OF LEU-354 AND PHE-358.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=23601177; DOI=10.1021/ja4024012;
RA Barandun J., Delley C.L., Ban N., Weber-Ban E.;
RT "Crystal structure of the complex between prokaryotic ubiquitin-like
RT protein and its ligase PafA.";
RL J. Am. Chem. Soc. 135:6794-6797(2013).
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, ECO:0000269|PubMed:22910360}.
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 ECO:0000269|PubMed:22910360};
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 -!- SUBUNIT: Interacts with the C-terminal half of the prokaryotic
CC ubiquitin-like protein Pup. {ECO:0000269|PubMed:22910360,
CC ECO:0000269|PubMed:23601177}.
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 -!- SEQUENCE CAUTION:
CC Sequence=BAB98887.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; BA000036; BAB98887.1; ALT_INIT; Genomic_DNA.
DR EMBL; BX927152; CAF21502.1; -; Genomic_DNA.
DR RefSeq; NP_600710.1; NC_003450.3.
DR RefSeq; WP_011265752.1; NC_006958.1.
DR PDB; 4B0T; X-ray; 2.16 A; A/B=1-482.
DR PDB; 4BJR; X-ray; 2.80 A; A/B=2-482.
DR PDBsum; 4B0T; -.
DR PDBsum; 4BJR; -.
DR AlphaFoldDB; Q8NQE1; -.
DR SMR; Q8NQE1; -.
DR STRING; 196627.cg1688; -.
DR DNASU; 3343131; -.
DR KEGG; cgb:cg1688; -.
DR KEGG; cgl:Cgl1494; -.
DR PATRIC; fig|196627.13.peg.1461; -.
DR eggNOG; COG0638; Bacteria.
DR HOGENOM; CLU_040524_0_1_11; -.
DR BRENDA; 3.5.1.119; 960.
DR BRENDA; 6.3.1.19; 960.
DR UniPathway; UPA00997; -.
DR UniPathway; UPA00998; -.
DR Proteomes; UP000000582; 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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Ligase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Ubl conjugation pathway.
FT CHAIN 1..482
FT /note="Pup--protein ligase"
FT /id="PRO_0000395908"
FT ACT_SITE 64
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:22910360"
FT BINDING 16
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111,
FT ECO:0000269|PubMed:23601177"
FT BINDING 60
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111,
FT ECO:0000269|PubMed:23601177"
FT BINDING 62
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111,
FT ECO:0000269|PubMed:23601177"
FT BINDING 70
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111,
FT ECO:0000269|PubMed:23601177"
FT BINDING 73
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111,
FT ECO:0000269|PubMed:23601177"
FT BINDING 440
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02111,
FT ECO:0000269|PubMed:23601177"
FT MUTAGEN 16
FT /note="E->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 18
FT /note="E->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 60
FT /note="R->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 64
FT /note="D->N: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 68
FT /note="H->A: Nearly abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 130
FT /note="H->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 199
FT /note="R->A: Reduces pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 201
FT /note="R->A: Highly reduces pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 211
FT /note="H->A: Reduces pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 221
FT /note="H->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 354
FT /note="L->E: Highly reduces pupylation."
FT /evidence="ECO:0000269|PubMed:23601177"
FT MUTAGEN 358
FT /note="F->E: Reduces pupylation."
FT /evidence="ECO:0000269|PubMed:23601177"
FT MUTAGEN 376
FT /note="L->E: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT MUTAGEN 440
FT /note="W->A: Abolishes pupylation."
FT /evidence="ECO:0000269|PubMed:22910360"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 13..18
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 20..24
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 28..31
FT /evidence="ECO:0007829|PDB:4BJR"
FT HELIX 34..48
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 79..106
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 112..116
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 129..136
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 148..159
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 163..165
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 186..194
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:4B0T"
FT TURN 214..216
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 217..222
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 231..250
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 259..261
FT /evidence="ECO:0007829|PDB:4B0T"
FT TURN 262..265
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 278..281
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 286..288
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 289..306
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 311..314
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 317..336
FT /evidence="ECO:0007829|PDB:4B0T"
FT TURN 340..345
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 347..362
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 369..377
FT /evidence="ECO:0007829|PDB:4B0T"
FT TURN 383..385
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 387..393
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 403..411
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 415..417
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 419..432
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 436..438
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 440..445
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 447..449
FT /evidence="ECO:0007829|PDB:4B0T"
FT STRAND 451..454
FT /evidence="ECO:0007829|PDB:4B0T"
FT HELIX 464..476
FT /evidence="ECO:0007829|PDB:4B0T"
SQ SEQUENCE 482 AA; 53801 MW; 41005A762B186ECD CRC64;
MSTVESALTR RIMGIETEYG LTFVDGDSKK LRPDEIARRM FRPIVEKYSS SNIFIPNGSR
LYLDVGSHPE YATAECDNLT QLINFEKAGD VIADRMAVDA EESLAKEDIA GQVYLFKNNV
DSVGNSYGCH ENYLVGRSMP LKALGKRLMP FLITRQLICG AGRIHHPNPL DKGESFPLGY
CISQRSDHVW EGVSSATTRS RPIINTRDEP HADSHSYRRL HVIVGDANMA EPSIALKVGS
TLLVLEMIEA DFGLPSLELA NDIASIREIS RDATGSTLLS LKDGTTMTAL QIQQVVFEHA
SKWLEQRPEP EFSGTSNTEM ARVLDLWGRM LKAIESGDFS EVDTEIDWVI KKKLIDRFIQ
RGNLGLDDPK LAQVDLTYHD IRPGRGLFSV LQSRGMIKRW TTDEAILAAV DTAPDTTRAH
LRGRILKAAD TLGVPVTVDW MRHKVNRPEP QSVELGDPFS AVNSEVDQLI EYMTVHAESY
RS
