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Database: UniProt/SWISS-PROT
Entry: DDL_VIBCH
LinkDB: DDL_VIBCH
Original site: DDL_VIBCH 
ID   DDL_VIBCH               Reviewed;         334 AA.
AC   Q9KM17;
DT   02-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   26-FEB-2020, entry version 116.
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=VC_A0572;
OS   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=243277;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX   PubMed=10952301; DOI=10.1038/35020000;
RA   Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA   Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA   Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA   Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA   Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA   Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT   "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT   cholerae.";
RL   Nature 406:477-483(2000).
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; AE003853; AAF96474.1; -; Genomic_DNA.
DR   PIR; A82443; A82443.
DR   RefSeq; NP_232962.1; NC_002506.1.
DR   RefSeq; WP_000169444.1; NZ_LT906615.1.
DR   PDB; 6DGI; X-ray; 2.30 A; A/B=1-334.
DR   PDBsum; 6DGI; -.
DR   SMR; Q9KM17; -.
DR   STRING; 243277.VC_A0572; -.
DR   DNASU; 2612376; -.
DR   EnsemblBacteria; AAF96474; AAF96474; VC_A0572.
DR   GeneID; 2612376; -.
DR   KEGG; vch:VCA0572; -.
DR   PATRIC; fig|243277.26.peg.3199; -.
DR   eggNOG; ENOG4105CPF; Bacteria.
DR   eggNOG; COG1181; LUCA.
DR   HOGENOM; CLU_039268_0_0_6; -.
DR   KO; K01921; -.
DR   OMA; YNLAGCK; -.
DR   BioCyc; VCHO:VCA0572-MONOMER; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000000584; 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; ISS:TIGR.
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; ISS:TIGR.
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   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation;
KW   Cytoplasm; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW   Peptidoglycan synthesis; Reference proteome.
FT   CHAIN           1..334
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_0000177901"
FT   DOMAIN          121..327
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   NP_BIND         151..206
FT                   /note="ATP"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           281
FT                   /note="Magnesium or manganese 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           294
FT                   /note="Magnesium or manganese 1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           294
FT                   /note="Magnesium or manganese 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   METAL           296
FT                   /note="Magnesium or manganese 2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   STRAND          4..11
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           17..31
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          37..45
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          48..51
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          56..60
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   TURN            61..64
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          65..67
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          72..74
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          76..81
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   TURN            85..90
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           91..99
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          103..105
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           108..115
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           117..126
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          134..137
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           142..155
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          156..162
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          171..174
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           177..179
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           180..188
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          192..198
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          203..212
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          215..218
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          222..225
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   TURN            229..231
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           234..238
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          245..249
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           255..271
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          276..284
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   STRAND          290..298
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           306..313
FT                   /evidence="ECO:0000244|PDB:6DGI"
FT   HELIX           318..331
FT                   /evidence="ECO:0000244|PDB:6DGI"
SQ   SEQUENCE   334 AA;  37318 MW;  B7581B22D766818B CRC64;
     MTKTTILLLC GGGSSEHEIS LVSANYIQQQ LELTPEFHVI RVEMKKEGWF SEQGALVYLD
     TNSATLNSDK ASYPIDFVVP CIHGFPGETG DIQSMLELAG IPYLGCGPEA SANSFNKITS
     KLWYDALDIP NTPYLFLTQN TPSSIDKAKQ AFGHWGSIFV KAARQGSSVG CYKVTTEDQI
     APAIEAAFGF SEQVLVEQAV KPRELEVSAY EMNGKLYISK PGEVIAPEGT FYSYEEKYSA
     NSHARTVLEA ENLTEKHKEL IQTYAERVFI HMKLRHLSRI DFFLTQEGQI YLNEVNTFPG
     MTPISMFPKM LEHNGHRFSE FLVQCVTNTL VNAK
//
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