DAPE_BORPE
ID DAPE_BORPE Reviewed; 379 AA.
AC Q7VXJ5; Q9ZEX1;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 96.
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=BP1763;
OS Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Alcaligenaceae; Bordetella.
OX NCBI_TaxID=257313;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Tohama I / BP338;
RX PubMed=10850974; DOI=10.1128/jb.182.13.3626-3631.2000;
RA Fuchs T.M., Schneider B., Krumbach K., Eggeling L., Gross R.;
RT "Characterization of a Bordetella pertussis diaminopimelate (DAP)
RT biosynthesis locus identifies dapC, a novel gene coding for an N-succinyl-
RT L,L-DAP aminotransferase.";
RL J. Bacteriol. 182:3626-3631(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tohama I / ATCC BAA-589 / NCTC 13251;
RX PubMed=12910271; DOI=10.1038/ng1227;
RA Parkhill J., Sebaihia M., Preston A., Murphy L.D., Thomson N.R.,
RA Harris D.E., Holden M.T.G., Churcher C.M., Bentley S.D., Mungall K.L.,
RA Cerdeno-Tarraga A.-M., Temple L., James K.D., Harris B., Quail M.A.,
RA Achtman M., Atkin R., Baker S., Basham D., Bason N., Cherevach I.,
RA Chillingworth T., Collins M., Cronin A., Davis P., Doggett J., Feltwell T.,
RA Goble A., Hamlin N., Hauser H., Holroyd S., Jagels K., Leather S.,
RA Moule S., Norberczak H., O'Neil S., Ormond D., Price C., Rabbinowitsch E.,
RA Rutter S., Sanders M., Saunders D., Seeger K., Sharp S., Simmonds M.,
RA Skelton J., Squares R., Squares S., Stevens K., Unwin L., Whitehead S.,
RA Barrell B.G., Maskell D.J.;
RT "Comparative analysis of the genome sequences of Bordetella pertussis,
RT Bordetella parapertussis and Bordetella bronchiseptica.";
RL Nat. Genet. 35:32-40(2003).
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; AJ009834; CAA08876.1; -; Genomic_DNA.
DR EMBL; BX640416; CAE42050.1; -; Genomic_DNA.
DR RefSeq; NP_880475.1; NC_002929.2.
DR RefSeq; WP_010930548.1; NZ_CP039022.1.
DR AlphaFoldDB; Q7VXJ5; -.
DR SMR; Q7VXJ5; -.
DR STRING; 257313.BP1763; -.
DR GeneID; 45388975; -.
DR KEGG; bpe:BP1763; -.
DR PATRIC; fig|257313.5.peg.1892; -.
DR eggNOG; COG0624; Bacteria.
DR HOGENOM; CLU_021802_4_0_4; -.
DR OMA; LNSHHDT; -.
DR UniPathway; UPA00034; UER00021.
DR Proteomes; UP000002676; 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 HAMAP; MF_01690; DapE; 1.
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..379
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000375479"
FT ACT_SITE 70
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT ACT_SITE 135
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 136
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT BINDING 350
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01690"
FT CONFLICT 119
FT /note="V -> G (in Ref. 1; CAA08876)"
FT /evidence="ECO:0000305"
FT CONFLICT 147
FT /note="C -> S (in Ref. 1; CAA08876)"
FT /evidence="ECO:0000305"
FT CONFLICT 315..327
FT /note="GLQAELSTTGGTS -> DCRPNSRPPAAHP (in Ref. 1;
FT CAA08876)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 379 AA; 40822 MW; 9F9FB0E18C8C7752 CRC64;
MTASAVLDLV KDLIARPSVT PDDVDCQMLL AQRLERIGFQ CETIARGGVT NLWARRGAGA
PLTVFAGHTD VVPPGPRDKW DSDPFVPTER DGFLYGRGAA DMKSSIAAFV VAAEEFVAVH
PEHPGSIALL ITSDEEGPAV DGTVIVCDEL RQRGEQLDYC IVGEPTSTEA LGDVCKNGRR
GSLSGRLLVK GVQGHVAYPH LARNPVHQLA PALTELVAIE WDQGNEYFPP TTFQVSNLHA
GTGATNVVPG EAVALFNFRF STASTPGQLK ARVHEVLDRH GLEYQLDWEL GGEPFLTPRG
SLTDALVSAI QAETGLQAEL STTGGTSDGR FIARICPQVI EFGPCNATIH KVNERIELSS
LAPLKNIYRR TLENLLLAD
