DDPX_SYNY3
ID DDPX_SYNY3 Reviewed; 247 AA.
AC P74268;
DT 27-APR-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 138.
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}; Synonyms=vanX;
GN OrderedLocusNames=slr1679;
OS Synechocystis sp. (strain PCC 6803 / Kazusa).
OC Bacteria; Cyanobacteria; Synechococcales; Merismopediaceae; Synechocystis;
OC unclassified Synechocystis.
OX NCBI_TaxID=1111708;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=8905231; DOI=10.1093/dnares/3.3.109;
RA Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y.,
RA Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T.,
RA Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.,
RA Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence analysis of the genome of the unicellular cyanobacterium
RT Synechocystis sp. strain PCC6803. II. Sequence determination of the entire
RT genome and assignment of potential protein-coding regions.";
RL DNA Res. 3:109-136(1996).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBCELLULAR LOCATION.
RC STRAIN=PCC 6803 / Kazusa;
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=1.6 mM for D-Ala-D-Ala {ECO:0000269|PubMed:9751644};
CC KM=8.3 mM for L-Ala-D-Ala {ECO:0000269|PubMed:9751644};
CC Note=kcat is 310 sec(-1) with D-Ala-D-Ala. kcat is 110 sec(-1) with
CC L-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; BA000022; BAA18362.1; -; Genomic_DNA.
DR PIR; S75903; S75903.
DR AlphaFoldDB; P74268; -.
DR SMR; P74268; -.
DR STRING; 1148.1653448; -.
DR PaxDb; P74268; -.
DR EnsemblBacteria; BAA18362; BAA18362; BAA18362.
DR KEGG; syn:slr1679; -.
DR eggNOG; COG2173; Bacteria.
DR InParanoid; P74268; -.
DR OMA; YGDQLWA; -.
DR PhylomeDB; P74268; -.
DR Proteomes; UP000001425; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016805; F:dipeptidase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
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 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..247
FT /note="D-alanyl-D-alanine dipeptidase"
FT /id="PRO_0000217838"
FT ACT_SITE 215
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT BINDING 140
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT BINDING 147
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT BINDING 218
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
FT SITE 84
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924"
SQ SEQUENCE 247 AA; 28437 MW; AA8C7774D6202B1B CRC64;
MSFDTPLKPY LAIPIQDCGE PLAPINLEGV KSLKPHPYAQ VGADYQGRSP YVLRTGVLKR
LDQARLTLAD IEPSWEILVF DAYRPIAVQQ FMVDHTFAEI VARDGLQGQV LTPEQKENIY
HQVYQIWAVP NNNPLTPPPH STGAALDITL LDDLGQPVDM GGEIDELSAR SLPNYYQTVE
PNSDRQRKEF EQYQRRRELL NTIMESAGFL RHPGEWWHFS QGDQLWAWQY NQRHPDHQKI
AYYGRVE
