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Database: UniProt
Entry: A1VST4
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ID   DDL_POLNA               Reviewed;         325 AA.
AC   A1VST4;
DT   10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT   06-FEB-2007, sequence version 1.
DT   26-NOV-2014, entry version 60.
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=Pnap_3415;
OS   Polaromonas naphthalenivorans (strain CJ2).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Polaromonas.
OX   NCBI_TaxID=365044;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CJ2;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H.,
RA   Pitluck S., Sims D.R., Brettin T., Bruce D., Han C., Tapia R.,
RA   Brainard J., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA   Kim E., Madsen E.L., Richardson P.;
RT   "Complete sequence of chromosome 1 of Polaromonas naphthalenivorans
RT   CJ2.";
RL   Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
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}.
CC   -!- SIMILARITY: Contains 1 ATP-grasp domain. {ECO:0000255|HAMAP-
CC       Rule:MF_00047}.
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DR   EMBL; CP000529; ABM38712.1; -; Genomic_DNA.
DR   RefSeq; YP_983633.1; NC_008781.1.
DR   ProteinModelPortal; A1VST4; -.
DR   SMR; A1VST4; 9-313.
DR   STRING; 365044.Pnap_3415; -.
DR   EnsemblBacteria; ABM38712; ABM38712; Pnap_3415.
DR   GeneID; 4688839; -.
DR   KEGG; pna:Pnap_3415; -.
DR   PATRIC; 22951551; VBIPolNap76733_4296.
DR   eggNOG; COG1181; -.
DR   HOGENOM; HOG000011592; -.
DR   KO; K01921; -.
DR   OMA; DRIQAND; -.
DR   OrthoDB; EOG6ND0KB; -.
DR   BioCyc; PNAP365044:GJ8X-3464-MONOMER; -.
DR   UniPathway; UPA00219; -.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-HAMAP.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-HAMAP.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR   GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-HAMAP.
DR   GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR   Gene3D; 3.30.1490.20; -; 1.
DR   Gene3D; 3.30.470.20; -; 2.
DR   Gene3D; 3.40.50.20; -; 1.
DR   HAMAP; MF_00047; Dala_Dala_lig; 1.
DR   InterPro; IPR011761; ATP-grasp.
DR   InterPro; IPR013815; ATP_grasp_subdomain_1.
DR   InterPro; IPR013816; ATP_grasp_subdomain_2.
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.
DR   PANTHER; PTHR23132; PTHR23132; 1.
DR   Pfam; PF07478; Dala_Dala_lig_C; 1.
DR   Pfam; PF01820; Dala_Dala_lig_N; 2.
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;
KW   Complete proteome; Cytoplasm; Ligase; Magnesium; Manganese;
KW   Metal-binding; Nucleotide-binding; Peptidoglycan synthesis;
KW   Reference proteome.
FT   CHAIN         1    325       D-alanine--D-alanine ligase.
FT                                /FTId=PRO_0000341150.
FT   DOMAIN      107    311       ATP-grasp. {ECO:0000255|HAMAP-
FT                                Rule:MF_00047}.
FT   NP_BIND     137    192       ATP. {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       264    264       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       278    278       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       278    278       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       280    280       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
SQ   SEQUENCE   325 AA;  34584 MW;  A75A4DD1D3D691F3 CRC64;
     MSPNPSSFGK VAVLMGGRSA EREISLMSGS GVVQALRSQG IDAHAFDPAE RDLGELKTGG
     FARCFIALHG RFGEDGTVQG ALELLGIPYT GSGVMASSMA IDKVMTKRLL LSESLPTPRY
     VLLRRGGYSP AQVDAIVDTL GLPLIVKPAR EGSSLGLSKV TERAAMAAAV ALAEKMDADI
     LCEQFISGDE VTCPVLGTGE QARALPVIRI VAPEGNYDYQ NKYFTDTTQY LVPCGLPAGE
     EAAIQQLVLQ AFRTLNCRGW ARADVMIDQA TRKPYLLEIN TSPGMTGHSL VPMSARAAGI
     SYEALCVEVL KTALLDHQPR DGSLP
//
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