DAPE_PARDP
ID DAPE_PARDP Reviewed; 382 AA.
AC A1B5Y2;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=Succinyl-diaminopimelate desuccinylase {ECO:0000255|HAMAP-Rule:MF_01690};
DE Short=SDAP desuccinylase {ECO:0000255|HAMAP-Rule:MF_01690};
DE EC=3.5.1.18 {ECO:0000255|HAMAP-Rule:MF_01690};
DE AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase {ECO:0000255|HAMAP-Rule:MF_01690};
GN Name=dapE {ECO:0000255|HAMAP-Rule:MF_01690}; OrderedLocusNames=Pden_2842;
OS Paracoccus denitrificans (strain Pd 1222).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=318586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Pd 1222;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S.,
RA Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M.,
RA Richardson P.;
RT "Complete sequence of chromosome 2 of Paracoccus denitrificans PD1222.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
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:0000255|HAMAP-Rule:MF_01690}.
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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01690};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01690};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01690};
CC Note=Binds 2 Zn(2+) or Co(2+) ions per subunit. {ECO:0000255|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:0000255|HAMAP-Rule:MF_01690}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01690}.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01690}.
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DR EMBL; CP000490; ABL70926.1; -; Genomic_DNA.
DR RefSeq; WP_011749117.1; NC_008687.1.
DR AlphaFoldDB; A1B5Y2; -.
DR SMR; A1B5Y2; -.
DR STRING; 318586.Pden_2842; -.
DR PRIDE; A1B5Y2; -.
DR EnsemblBacteria; ABL70926; ABL70926; Pden_2842.
DR KEGG; pde:Pden_2842; -.
DR eggNOG; COG0624; Bacteria.
DR HOGENOM; CLU_021802_4_0_5; -.
DR OMA; LNSHHDT; -.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000000361; Chromosome 2.
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 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 3: Inferred from homology;
KW Amino-acid biosynthesis; Cobalt; Diaminopimelate biosynthesis; Hydrolase;
KW Lysine biosynthesis; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..382
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000375639"
FT ACT_SITE 72
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT ACT_SITE 137
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 70
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 138
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 166
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 355
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
SQ SEQUENCE 382 AA; 41001 MW; 1DABB2625D970C60 CRC64;
MTPIPDPAQL TARLIRCASV TPDEGGALVL LADVLGAAGF ECHRVDREGV PNLFARWGAQ
GARTFGFNGH TDVVPPGDPA SWTHPPFSGH EAEGWIWGRG ATDMKSGVAA FAAAAIGFVT
QTPPPDGAVI LAITGDEEGP GKHGTRALLD WMAARGERMD VCIVGEPSNP DRMGEMIKIG
RRGSMTLQIE AHGIQGHAAY PHRARNPIHA LLRLLHELTD APLDEGTEHF DPSGLQVTTV
DCGNPASNVI PERARAVINI RFNDAHTAES LDRMIRARAA AISAETKVDF AISTDVSGES
FLTAPGPFVD LVAGVVREET GLDPVLSTSG GTSDARFVKD HCPVLEFGLV GHFMHQVDER
VPADQVRQLA RIYRRILERY FA
