DAPE_VIBCH
ID DAPE_VIBCH Reviewed; 377 AA.
AC Q9KQ52;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Succinyl-diaminopimelate desuccinylase;
DE Short=SDAP desuccinylase;
DE EC=3.5.1.18;
DE AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase;
GN Name=dapE; OrderedLocusNames=VC_2152;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
RN [2] {ECO:0007744|PDB:4ONW, ECO:0007744|PDB:4OP4}
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH ZINC IONS, AND
RP COFACTOR.
RA Nocek B., Makowska-Grzyska M., Gu M., Jedrzejczak R., Anderson W.F.,
RA Joachimiak A.;
RT "Crystal structure of the catalytic domain of dape protein V.Cholerea in
RT the Zn bound form.";
RL Submitted (JUL-2011) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic
CC acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP),
CC an intermediate involved in the bacterial biosynthesis of lysine and
CC meso-diaminopimelic acid, an essential component of bacterial cell
CC walls. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-
CC 2,6-diaminoheptanedioate + succinate; Xref=Rhea:RHEA:22608,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:30031, ChEBI:CHEBI:57609,
CC ChEBI:CHEBI:58087; EC=3.5.1.18;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000269|Ref.2};
CC Note=Binds 2 Zn(2+) ion per subunit. {ECO:0000269|Ref.2};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate
CC (succinylase route): step 3/3.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC {ECO:0000305}.
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; AE003852; AAF95297.1; -; Genomic_DNA.
DR PIR; C82113; C82113.
DR RefSeq; NP_231783.1; NC_002505.1.
DR RefSeq; WP_000132407.1; NZ_LT906614.1.
DR PDB; 4ONW; X-ray; 1.65 A; A/B=2-181, A/B=295-377.
DR PDB; 4OP4; X-ray; 1.65 A; A/B=2-181, A/B=295-377.
DR PDBsum; 4ONW; -.
DR PDBsum; 4OP4; -.
DR AlphaFoldDB; Q9KQ52; -.
DR SMR; Q9KQ52; -.
DR STRING; 243277.VC_2152; -.
DR DNASU; 2613288; -.
DR EnsemblBacteria; AAF95297; AAF95297; VC_2152.
DR GeneID; 57740769; -.
DR KEGG; vch:VC_2152; -.
DR PATRIC; fig|243277.26.peg.2055; -.
DR eggNOG; COG0624; Bacteria.
DR HOGENOM; CLU_021802_4_0_6; -.
DR OMA; LNSHHDT; -.
DR BioCyc; VCHO:VC2152-MON; -.
DR BRENDA; 3.5.1.18; 6626.
DR UniPathway; UPA00034; UER00021.
DR EvolutionaryTrace; Q9KQ52; -.
DR Proteomes; UP000000584; Chromosome 1.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0050897; F:cobalt ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009014; F:succinyl-diaminopimelate desuccinylase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0043093; P:FtsZ-dependent cytokinesis; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
DR HAMAP; MF_01690; DapE; 1.
DR InterPro; IPR001261; ArgE/DapE_CS.
DR InterPro; IPR036264; Bact_exopeptidase_dim_dom.
DR InterPro; IPR005941; DapE_proteobac.
DR InterPro; IPR002933; Peptidase_M20.
DR InterPro; IPR011650; Peptidase_M20_dimer.
DR Pfam; PF07687; M20_dimer; 1.
DR Pfam; PF01546; Peptidase_M20; 1.
DR SUPFAM; SSF55031; SSF55031; 1.
DR TIGRFAMs; TIGR01246; dapE_proteo; 1.
DR PROSITE; PS00759; ARGE_DAPE_CPG2_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cobalt;
KW Diaminopimelate biosynthesis; Hydrolase; Lysine biosynthesis;
KW Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..377
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000375766"
FT ACT_SITE 70
FT /evidence="ECO:0000250"
FT ACT_SITE 135
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:4OP4"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:4OP4"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:4OP4"
FT BINDING 136
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:4OP4"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:4OP4"
FT BINDING 350
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:4OP4"
FT HELIX 5..15
FT /evidence="ECO:0007829|PDB:4ONW"
FT HELIX 26..36
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 40..46
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 49..56
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 58..60
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:4ONW"
FT HELIX 77..79
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 88..90
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 93..96
FT /evidence="ECO:0007829|PDB:4ONW"
FT TURN 97..102
FT /evidence="ECO:0007829|PDB:4ONW"
FT HELIX 103..119
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 124..133
FT /evidence="ECO:0007829|PDB:4ONW"
FT HELIX 142..152
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 167..170
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 173..177
FT /evidence="ECO:0007829|PDB:4ONW"
FT HELIX 301..314
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 319..323
FT /evidence="ECO:0007829|PDB:4ONW"
FT HELIX 327..335
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 338..341
FT /evidence="ECO:0007829|PDB:4ONW"
FT TURN 347..350
FT /evidence="ECO:0007829|PDB:4ONW"
FT STRAND 355..357
FT /evidence="ECO:0007829|PDB:4ONW"
FT HELIX 358..376
FT /evidence="ECO:0007829|PDB:4ONW"
SQ SEQUENCE 377 AA; 40749 MW; 7BB30F14331AE32C CRC64;
MTDSPVLALA KELISRQSVT PADAGCQDLM IERLKALGFE IESMVFEDTT NFWARRGTQS
PLFVFAGHTD VVPAGPLSQW HTPPFEPTVI DGFLHGRGAA DMKGSLACMI VAVERFIAEH
PDHQGSIGFL ITSDEEGPFI NGTVRVVETL MARNELIDMC IVGEPSSTLA VGDVVKNGRR
GSITGDLKVK GTQGHVAYPH LANNPVHKAL PALAELAATQ WDEGNAYFPP TSFQIPNLQA
GTGASNVIPG EFDVQFNFRF STELTDEEIK RRVHSVLDAH GLDYDVKWTL SGQPFLTDTG
ELLAAVVAAV EEVNHQAPAL LTTGGTSDGR FIAQMGAQVV ELGPVNATIH KVNECVRIAD
LEKLTDMYQK TLNHLLG
