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Database: UniProt/SWISS-PROT
Entry: DDL_VIBPA
LinkDB: DDL_VIBPA
Original site: DDL_VIBPA 
ID   DDL_VIBPA               Reviewed;         329 AA.
AC   Q87HS0;
DT   11-JUL-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2003, sequence version 1.
DT   26-FEB-2020, entry version 103.
DE   RecName: Full=D-alanine--D-alanine ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE            EC=6.3.2.4 {ECO:0000255|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-Ala-D-Ala ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-alanylalanine synthetase {ECO:0000255|HAMAP-Rule:MF_00047};
GN   Name=ddl {ECO:0000255|HAMAP-Rule:MF_00047}; OrderedLocusNames=VPA0886;
OS   Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=223926;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=RIMD 2210633;
RX   PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA   Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA   Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA   Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT   "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT   distinct from that of V. cholerae.";
RL   Lancet 361:743-749(2003).
CC   -!- FUNCTION: Cell wall formation. {ECO:0000255|HAMAP-Rule:MF_00047}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) +
CC         phosphate; Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:57416,
CC         ChEBI:CHEBI:57822, ChEBI:CHEBI:456216; EC=6.3.2.4;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00047};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Binds 2 magnesium or manganese ions per subunit. {ECO:0000250};
CC   -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC       {ECO:0000255|HAMAP-Rule:MF_00047}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00047}.
CC   -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00047}.
DR   EMBL; BA000032; BAC62229.1; -; Genomic_DNA.
DR   RefSeq; NP_800396.1; NC_004605.1.
DR   RefSeq; WP_005455294.1; NC_004605.1.
DR   SMR; Q87HS0; -.
DR   STRING; 223926.28809187; -.
DR   EnsemblBacteria; BAC62229; BAC62229; BAC62229.
DR   GeneID; 1191575; -.
DR   KEGG; vpa:VPA0886; -.
DR   PATRIC; fig|223926.6.peg.3819; -.
DR   eggNOG; ENOG4105CPF; Bacteria.
DR   eggNOG; COG1181; LUCA.
DR   HOGENOM; CLU_039268_0_0_6; -.
DR   KO; K01921; -.
DR   OMA; YNLAGCK; -.
DR   BioCyc; VPAR223926:G1GTB-4118-MONOMER; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000002493; Chromosome 2.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR   GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR   Gene3D; 3.30.1490.20; -; 1.
DR   HAMAP; MF_00047; Dala_Dala_lig; 1.
DR   InterPro; IPR011761; ATP-grasp.
DR   InterPro; IPR013815; ATP_grasp_subdomain_1.
DR   InterPro; IPR000291; D-Ala_lig_Van_CS.
DR   InterPro; IPR005905; D_ala_D_ala.
DR   InterPro; IPR011095; Dala_Dala_lig_C.
DR   InterPro; IPR011127; Dala_Dala_lig_N.
DR   InterPro; IPR016185; PreATP-grasp_dom_sf.
DR   Pfam; PF07478; Dala_Dala_lig_C; 1.
DR   Pfam; PF01820; Dala_Dala_lig_N; 1.
DR   PIRSF; PIRSF039102; Ddl/VanB; 1.
DR   SUPFAM; SSF52440; SSF52440; 1.
DR   TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 1.
DR   PROSITE; PS50975; ATP_GRASP; 1.
DR   PROSITE; PS00843; DALA_DALA_LIGASE_1; 1.
DR   PROSITE; PS00844; DALA_DALA_LIGASE_2; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Cell shape; Cell wall biogenesis/degradation; Cytoplasm;
KW   Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW   Peptidoglycan synthesis; Reference proteome.
FT   CHAIN           1..329
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_0000177902"
FT   DOMAIN          120..326
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   NP_BIND         150..205
FT                   /note="ATP"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           280
FT                   /note="Magnesium or manganese 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           293
FT                   /note="Magnesium or manganese 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           293
FT                   /note="Magnesium or manganese 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           295
FT                   /note="Magnesium or manganese 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ   SEQUENCE   329 AA;  36957 MW;  00BD14677D80A2D5 CRC64;
     MIKNILLLCG GGSSEHEISL LSANFVEQQL NLIQNVKVTR VEIKNEGWVT DQGELVYLDL
     NTKQLCSNES NQTIDFIVPC IHGFPGETGD IQSLFEIAGI PYLGCGPEAS SNSFNKITSK
     LWYDALDIPN TPYLFLTRND EHAHRQAEQA FEKWGKVFVK AARQGSSVGC YSVAEKQAIA
     KAVNDAFGYS DQVLVEKAVK PRELEVAAYE MNGELHITKP GEVIAPDGAF YSYDEKYSSS
     SHSLTEVEAK NLTQEQIDKI RHASETVFKQ MNLRHLSRID FFLTEDNEIY LNEVNTFPGM
     TPISMFPKML QNNGHKFHEF LEDCINSAK
//
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