ID E1SKM5_PANVC Unreviewed; 375 AA.
AC E1SKM5;
DT 30-NOV-2010, integrated into UniProtKB/TrEMBL.
DT 30-NOV-2010, sequence version 1.
DT 27-MAR-2024, entry version 78.
DE RecName: Full=Succinyl-diaminopimelate desuccinylase {ECO:0000256|ARBA:ARBA00022391, ECO:0000256|HAMAP-Rule:MF_01690};
DE Short=SDAP desuccinylase {ECO:0000256|HAMAP-Rule:MF_01690};
DE EC=3.5.1.18 {ECO:0000256|ARBA:ARBA00011921, ECO:0000256|HAMAP-Rule:MF_01690};
DE AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase {ECO:0000256|ARBA:ARBA00031891, ECO:0000256|HAMAP-Rule:MF_01690};
GN Name=dapE {ECO:0000256|HAMAP-Rule:MF_01690,
GN ECO:0000313|EMBL:ADO10402.1};
GN OrderedLocusNames=Pvag_2229 {ECO:0000313|EMBL:ADO10402.1};
OS Pantoea vagans (strain C9-1) (Pantoea agglomerans (strain C9-1)).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Erwiniaceae; Pantoea.
OX NCBI_TaxID=712898 {ECO:0000313|EMBL:ADO10402.1, ECO:0000313|Proteomes:UP000006631};
RN [1] {ECO:0000313|EMBL:ADO10402.1, ECO:0000313|Proteomes:UP000006631}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C9-1 {ECO:0000313|EMBL:ADO10402.1,
RC ECO:0000313|Proteomes:UP000006631};
RX PubMed=20952567; DOI=10.1128/JB.01122-10;
RA Smits T.H., Rezzonico F., Kamber T., Goesmann A., Ishimaru C.A.,
RA Stockwell V.O., Frey J.E., Duffy B.;
RT "The genome sequence of the biocontrol agent Pantoea vagans strain C9-1.";
RL J. Bacteriol. 192:6486-6487(2010).
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:0000256|HAMAP-Rule:MF_01690}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-succinyl-(2S,6S)-2,6-diaminoheptanedioate =
CC (2S,6S)-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 Evidence={ECO:0000256|ARBA:ARBA00001246, ECO:0000256|HAMAP-
CC Rule:MF_01690};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000256|ARBA:ARBA00001941};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01690};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01690};
CC Note=Binds 2 Zn(2+) or Co(2+) ions per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_01690};
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. {ECO:0000256|ARBA:ARBA00005130,
CC ECO:0000256|HAMAP-Rule:MF_01690}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|ARBA:ARBA00011738, ECO:0000256|HAMAP-
CC Rule:MF_01690}.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC {ECO:0000256|ARBA:ARBA00006746, ECO:0000256|HAMAP-Rule:MF_01690}.
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DR EMBL; CP002206; ADO10402.1; -; Genomic_DNA.
DR RefSeq; WP_013358682.1; NC_014562.1.
DR AlphaFoldDB; E1SKM5; -.
DR MEROPS; M20.010; -.
DR GeneID; 58737209; -.
DR KEGG; pva:Pvag_2229; -.
DR eggNOG; COG0624; Bacteria.
DR HOGENOM; CLU_021802_4_0_6; -.
DR OrthoDB; 9809784at2; -.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000006631; Chromosome.
DR GO; GO:0050897; F:cobalt ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009014; F:succinyl-diaminopimelate desuccinylase activity; IEA:UniProtKB-UniRule.
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:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
DR CDD; cd03891; M20_DapE_proteobac; 1.
DR Gene3D; 3.40.630.10; Zn peptidases; 2.
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 NCBIfam; TIGR01246; dapE_proteo; 1.
DR PANTHER; PTHR43808; ACETYLORNITHINE DEACETYLASE; 1.
DR PANTHER; PTHR43808:SF3; ACETYLORNITHINE DEACETYLASE-RELATED; 1.
DR Pfam; PF07687; M20_dimer; 1.
DR Pfam; PF01546; Peptidase_M20; 1.
DR SUPFAM; SSF55031; Bacterial exopeptidase dimerisation domain; 1.
DR SUPFAM; SSF53187; Zn-dependent exopeptidases; 1.
DR PROSITE; PS00758; ARGE_DAPE_CPG2_1; 1.
DR PROSITE; PS00759; ARGE_DAPE_CPG2_2; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW Rule:MF_01690};
KW Cobalt {ECO:0000256|ARBA:ARBA00023285, ECO:0000256|HAMAP-Rule:MF_01690};
KW Diaminopimelate biosynthesis {ECO:0000256|ARBA:ARBA00022915,
KW ECO:0000256|HAMAP-Rule:MF_01690};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_01690};
KW Lysine biosynthesis {ECO:0000256|ARBA:ARBA00023154, ECO:0000256|HAMAP-
KW Rule:MF_01690};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01690};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01690}.
FT DOMAIN 175..282
FT /note="Peptidase M20 dimerisation"
FT /evidence="ECO:0000259|Pfam:PF07687"
FT ACT_SITE 68
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT ACT_SITE 133
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 134
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
FT BINDING 348
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01690"
SQ SEQUENCE 375 AA; 41330 MW; 065390AE714FA9DF CRC64;
MFCPVIELTQ QLIRRPSLSP DDAGCQALLI ARLEAIGFKI ETMNIDDTLN FWATRGEGET
LAFAGHTDVV PPGDASRWIN PPFEPTIRDG MLFGRGAADM KGSLAAMVVA AERFVAVRPN
HRGRLAFMIT SDEEASGTNG TVKVVERLMA RRERLDYCLV GEPSSTEVVG DVVKNGRRGS
ITANLTVHGV QGHVAYPHLA DNPVHRAMPA LTELVATEWD QGNEFFPATS MQIANVQAGT
GSNNVIPGEL FVQFNFRFST ELTDEMIRQR VAELLDRHQL RYTIEWKLSG QPFLTSRGKL
VDAVVKAVAH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI NECVKASDLQ
MLSRMYQRIM EQLIA
//
