DAPE_ECOLI
ID DAPE_ECOLI Reviewed; 375 AA.
AC P0AED7; P24176;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Succinyl-diaminopimelate desuccinylase;
DE Short=SDAP desuccinylase {ECO:0000303|PubMed:3276674};
DE EC=3.5.1.18 {ECO:0000269|PubMed:3276674};
DE AltName: Full=N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase;
GN Name=dapE; Synonyms=msgB; OrderedLocusNames=b2472, JW2456;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1644752; DOI=10.1128/jb.174.16.5265-5271.1992;
RA Bouvier J., Richaud C., Higgins W., Bogler O., Stragier S.;
RT "Cloning, characterization, and expression of the dapE gene of Escherichia
RT coli.";
RL J. Bacteriol. 174:5265-5271(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1644751; DOI=10.1128/jb.174.16.5258-5264.1992;
RA Wu B., Georgopoulos C., Ang D.;
RT "The essential Escherichia coli msgB gene, a multicopy suppressor of a
RT temperature-sensitive allele of the heat shock gene grpE, is identical to
RT dapE.";
RL J. Bacteriol. 174:5258-5264(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP FUNCTION, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND CATALYTIC
RP ACTIVITY.
RX PubMed=3276674; DOI=10.1016/s0021-9258(19)77924-1;
RA Lin Y.K., Myhrman R., Schrag M.L., Gelb M.H.;
RT "Bacterial N-succinyl-L-diaminopimelic acid desuccinylase. Purification,
RT partial characterization, and substrate specificity.";
RL J. Biol. Chem. 263:1622-1627(1988).
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:0000269|PubMed:3276674}.
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 Evidence={ECO:0000269|PubMed:3276674};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:3276674};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:3276674};
CC Note=Binds 2 Zn(2+) or Co(2+) ions per subunit.
CC {ECO:0000269|PubMed:3276674};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.41 mM for L,L-SDAP (in the presence of Zn(2+) at pH 7.0)
CC {ECO:0000269|PubMed:3276674};
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:0000269|PubMed:3276674}.
CC -!- MISCELLANEOUS: DapE/msgB is a multicopy suppressor of a temperature-
CC sensitive allele of the heat shock gene grpE.
CC -!- SIMILARITY: Belongs to the peptidase M20A family. DapE subfamily.
CC {ECO:0000305}.
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DR EMBL; S41760; AAB22798.1; -; Genomic_DNA.
DR EMBL; X57403; CAA40665.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75525.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16346.1; -; Genomic_DNA.
DR PIR; A42959; A42959.
DR RefSeq; NP_416967.1; NC_000913.3.
DR RefSeq; WP_001277801.1; NZ_STEB01000051.1.
DR AlphaFoldDB; P0AED7; -.
DR SMR; P0AED7; -.
DR BioGRID; 4261716; 4.
DR BioGRID; 852610; 3.
DR IntAct; P0AED7; 6.
DR STRING; 511145.b2472; -.
DR MEROPS; M20.010; -.
DR jPOST; P0AED7; -.
DR PaxDb; P0AED7; -.
DR PRIDE; P0AED7; -.
DR EnsemblBacteria; AAC75525; AAC75525; b2472.
DR EnsemblBacteria; BAA16346; BAA16346; BAA16346.
DR GeneID; 66673666; -.
DR GeneID; 948313; -.
DR KEGG; ecj:JW2456; -.
DR KEGG; eco:b2472; -.
DR PATRIC; fig|1411691.4.peg.4268; -.
DR EchoBASE; EB0204; -.
DR eggNOG; COG0624; Bacteria.
DR HOGENOM; CLU_021802_4_0_6; -.
DR InParanoid; P0AED7; -.
DR OMA; LNSHHDT; -.
DR PhylomeDB; P0AED7; -.
DR BioCyc; EcoCyc:MON0-1981; -.
DR BioCyc; MetaCyc:MON0-1981; -.
DR SABIO-RK; P0AED7; -.
DR UniPathway; UPA00034; UER00021.
DR PRO; PR:P0AED7; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0032153; C:cell division site; IDA:EcoCyc.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0050897; F:cobalt ion binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0009014; F:succinyl-diaminopimelate desuccinylase activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
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; IMP:EcoCyc.
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; PS00758; ARGE_DAPE_CPG2_1; 1.
DR PROSITE; PS00759; ARGE_DAPE_CPG2_2; 1.
PE 1: Evidence at protein level;
KW Amino-acid biosynthesis; Cobalt; Diaminopimelate biosynthesis; Hydrolase;
KW Lysine biosynthesis; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..375
FT /note="Succinyl-diaminopimelate desuccinylase"
FT /id="PRO_0000185261"
FT ACT_SITE 68
FT /evidence="ECO:0000250"
FT ACT_SITE 133
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 134
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 162
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 348
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 375 AA; 41269 MW; 181F43D05E88C20E CRC64;
MSCPVIELTQ QLIRRPSLSP DDAGCQALLI ERLQAIGFTV ERMDFADTQN FWAWRGQGET
LAFAGHTDVV PPGDADRWIN PPFEPTIRDG MLFGRGAADM KGSLAAMVVA AERFVAQHPN
HTGRLAFLIT SDEEASAHNG TVKVVEALMA RNERLDYCLV GEPSSIEVVG DVVKNGRRGS
LTCNLTIHGV QGHVAYPHLA DNPVHRAAPF LNELVAIEWD QGNEFFPATS MQIANIQAGT
GSNNVIPGEL FVQFNFRFST ELTDEMIKAQ VLALLEKHQL RYTVDWWLSG QPFLTARGKL
VDAVVNAVEH YNEIKPQLLT TGGTSDGRFI ARMGAQVVEL GPVNATIHKI NECVNAADLQ
LLARMYQRIM EQLVA
