DDPX_ECOLI
ID DDPX_ECOLI Reviewed; 193 AA.
AC P77790;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=D-alanyl-D-alanine dipeptidase {ECO:0000255|HAMAP-Rule:MF_01924};
DE Short=D-Ala-D-Ala dipeptidase {ECO:0000255|HAMAP-Rule:MF_01924};
DE EC=3.4.13.22 {ECO:0000255|HAMAP-Rule:MF_01924};
GN Name=ddpX {ECO:0000255|HAMAP-Rule:MF_01924};
GN Synonyms=vanX {ECO:0000303|PubMed:9751644}, yddT;
GN OrderedLocusNames=b1488, JW1483;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [2]
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 [3]
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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBCELLULAR LOCATION.
RX PubMed=9751644; DOI=10.1016/s1074-5521(98)90005-9;
RA Lessard I.A.D., Pratt S.D., McCafferty D.G., Bussiere D.E., Hutchins C.,
RA Wanner B.L., Katz L., Walsh C.T.;
RT "Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in
RT Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of
RT catalytic efficiency, stereoselectivity and regulation with implications
RT for function.";
RL Chem. Biol. 5:489-504(1998).
CC -!- FUNCTION: Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide. May
CC have a role in cell-wall turnover. {ECO:0000255|HAMAP-Rule:MF_01924,
CC ECO:0000269|PubMed:9751644}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-alanyl-D-alanine + H2O = 2 D-alanine; Xref=Rhea:RHEA:20661,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:57416, ChEBI:CHEBI:57822;
CC EC=3.4.13.22; Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
CC ECO:0000269|PubMed:9751644};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000305|PubMed:9751644};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000305|PubMed:9751644};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.4 mM for D-Ala-D-Ala {ECO:0000269|PubMed:9751644};
CC KM=550 mM for L-Ala-D-Ala {ECO:0000269|PubMed:9751644};
CC Note=kcat is 170 sec(-1) with D-Ala-D-Ala. kcat is 70 sec(-1) with L-
CC Ala-D-Ala.;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:9751644}.
CC -!- SIMILARITY: Belongs to the peptidase M15D family. {ECO:0000255|HAMAP-
CC Rule:MF_01924}.
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DR EMBL; U00096; AAC74561.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15143.1; -; Genomic_DNA.
DR PIR; C64902; C64902.
DR RefSeq; NP_416005.1; NC_000913.3.
DR RefSeq; WP_001285833.1; NZ_SSZK01000038.1.
DR AlphaFoldDB; P77790; -.
DR SMR; P77790; -.
DR BioGRID; 4259362; 255.
DR DIP; DIP-9418N; -.
DR STRING; 511145.b1488; -.
DR PaxDb; P77790; -.
DR PRIDE; P77790; -.
DR EnsemblBacteria; AAC74561; AAC74561; b1488.
DR EnsemblBacteria; BAA15143; BAA15143; BAA15143.
DR GeneID; 945532; -.
DR KEGG; ecj:JW1483; -.
DR KEGG; eco:b1488; -.
DR PATRIC; fig|1411691.4.peg.779; -.
DR EchoBASE; EB3552; -.
DR eggNOG; COG2173; Bacteria.
DR HOGENOM; CLU_060744_1_2_6; -.
DR InParanoid; P77790; -.
DR OMA; IRTEWWH; -.
DR PhylomeDB; P77790; -.
DR BioCyc; EcoCyc:G6782-MON; -.
DR BioCyc; MetaCyc:G6782-MON; -.
DR PRO; PR:P77790; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016805; F:dipeptidase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0009046; F:zinc D-Ala-D-Ala carboxypeptidase activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0042594; P:response to starvation; TAS:EcoCyc.
DR Gene3D; 3.30.1380.10; -; 1.
DR HAMAP; MF_01924; A_A_dipeptidase; 1.
DR InterPro; IPR000755; A_A_dipeptidase.
DR InterPro; IPR009045; Hedgehog_sig/DD-Pept_Zn-bd_sf.
DR Pfam; PF01427; Peptidase_M15; 1.
DR PIRSF; PIRSF026671; AA_dipeptidase; 1.
DR SUPFAM; SSF55166; SSF55166; 1.
PE 1: Evidence at protein level;
KW Cell wall biogenesis/degradation; Cytoplasm; Dipeptidase; Hydrolase;
KW Metal-binding; Metalloprotease; Protease; Reference proteome; Zinc.
FT CHAIN 1..193
FT /note="D-alanyl-D-alanine dipeptidase"
FT /id="PRO_0000217837"
FT ACT_SITE 162
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT BINDING 98
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT BINDING 105
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT BINDING 165
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT SITE 71
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
SQ SEQUENCE 193 AA; 21213 MW; 6933AAD3FCCD684F CRC64;
MSDTTELVDL AVIFPDLEIE LKYACADNIT GKAIYQQARC LLHKDAITAL AKSISIAQLS
GLQLVIYDAY RPQQAQAMLW QACPDPQYVV DVTVGSNHSR GTAIDLTLRD EHGNILDMGA
GFDEMHERSH AYHPSVPPAA QRNRLLLNAI MTGGGFVGIS SEWWHFELPQ AASYPLLADQ
FSCFISPGTQ HVS
