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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   12-SEP-2018, entry version 107.
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};
GN   OrderedLocusNames=VC_A0572;
OS   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales;
OC   Vibrionaceae; 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.,
RA   Gill S.R., Nelson K.E., Read T.D., Tettelin H., Richardson D.L.,
RA   Ermolaeva M.D., Vamathevan J.J., Bass S., Qin H., Dragoi I.,
RA   Sellers P., McDonald L.A., Utterback T.R., Fleischmann R.D.,
RA   Nierman W.C., White O., Salzberg S.L., Smith H.O., Colwell R.R.,
RA   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: ATP + 2 D-alanine = ADP + phosphate + D-
CC       alanyl-D-alanine. {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.
CC       {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; NC_002506.1.
DR   PDB; 6DGI; X-ray; 2.30 A; A/B=1-334.
DR   PDBsum; 6DGI; -.
DR   ProteinModelPortal; Q9KM17; -.
DR   SMR; Q9KM17; -.
DR   STRING; 243277.VCA0572; -.
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   KO; K01921; -.
DR   OMA; RCDFFVI; -.
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;
KW   Cell wall biogenesis/degradation; Complete proteome; Cytoplasm;
KW   Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW   Peptidoglycan synthesis; Reference proteome.
FT   CHAIN         1    334       D-alanine--D-alanine ligase.
FT                                /FTId=PRO_0000177901.
FT   DOMAIN      121    327       ATP-grasp. {ECO:0000255|HAMAP-
FT                                Rule:MF_00047}.
FT   NP_BIND     151    206       ATP. {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       281    281       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       294    294       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       294    294       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       296    296       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   STRAND        4     11       {ECO:0000244|PDB:6DGI}.
FT   HELIX        17     31       {ECO:0000244|PDB:6DGI}.
FT   STRAND       37     45       {ECO:0000244|PDB:6DGI}.
FT   STRAND       48     51       {ECO:0000244|PDB:6DGI}.
FT   STRAND       56     60       {ECO:0000244|PDB:6DGI}.
FT   TURN         61     64       {ECO:0000244|PDB:6DGI}.
FT   STRAND       65     67       {ECO:0000244|PDB:6DGI}.
FT   STRAND       72     74       {ECO:0000244|PDB:6DGI}.
FT   STRAND       76     81       {ECO:0000244|PDB:6DGI}.
FT   TURN         85     90       {ECO:0000244|PDB:6DGI}.
FT   HELIX        91     99       {ECO:0000244|PDB:6DGI}.
FT   STRAND      103    105       {ECO:0000244|PDB:6DGI}.
FT   HELIX       108    115       {ECO:0000244|PDB:6DGI}.
FT   HELIX       117    126       {ECO:0000244|PDB:6DGI}.
FT   STRAND      134    137       {ECO:0000244|PDB:6DGI}.
FT   HELIX       142    155       {ECO:0000244|PDB:6DGI}.
FT   STRAND      156    162       {ECO:0000244|PDB:6DGI}.
FT   STRAND      171    174       {ECO:0000244|PDB:6DGI}.
FT   HELIX       177    179       {ECO:0000244|PDB:6DGI}.
FT   HELIX       180    188       {ECO:0000244|PDB:6DGI}.
FT   STRAND      192    198       {ECO:0000244|PDB:6DGI}.
FT   STRAND      203    212       {ECO:0000244|PDB:6DGI}.
FT   STRAND      215    218       {ECO:0000244|PDB:6DGI}.
FT   STRAND      222    225       {ECO:0000244|PDB:6DGI}.
FT   TURN        229    231       {ECO:0000244|PDB:6DGI}.
FT   HELIX       234    238       {ECO:0000244|PDB:6DGI}.
FT   STRAND      245    249       {ECO:0000244|PDB:6DGI}.
FT   HELIX       255    271       {ECO:0000244|PDB:6DGI}.
FT   STRAND      276    284       {ECO:0000244|PDB:6DGI}.
FT   STRAND      290    298       {ECO:0000244|PDB:6DGI}.
FT   HELIX       306    313       {ECO:0000244|PDB:6DGI}.
FT   HELIX       318    331       {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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