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Database: UniProt
Entry: Q03ZI1
LinkDB: Q03ZI1
Original site: Q03ZI1 
ID   DDL_LEUMM               Reviewed;         377 AA.
AC   Q03ZI1;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   14-NOV-2006, sequence version 1.
DT   16-JAN-2019, entry version 91.
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=LEUM_0264;
OS   Leuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 /
OS   NCDO 523).
OC   Bacteria; Firmicutes; Bacilli; Lactobacillales; Leuconostocaceae;
OC   Leuconostoc.
OX   NCBI_TaxID=203120;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 8293 / NCDO 523;
RX   PubMed=17030793; DOI=10.1073/pnas.0607117103;
RA   Makarova K.S., Slesarev A., Wolf Y.I., Sorokin A., Mirkin B.,
RA   Koonin E.V., Pavlov A., Pavlova N., Karamychev V., Polouchine N.,
RA   Shakhova V., Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K.,
RA   Goodstein D.M., Hawkins T., Plengvidhya V., Welker D., Hughes J.,
RA   Goh Y., Benson A., Baldwin K., Lee J.-H., Diaz-Muniz I., Dosti B.,
RA   Smeianov V., Wechter W., Barabote R., Lorca G., Altermann E.,
RA   Barrangou R., Ganesan B., Xie Y., Rawsthorne H., Tamir D., Parker C.,
RA   Breidt F., Broadbent J.R., Hutkins R., O'Sullivan D., Steele J.,
RA   Unlu G., Saier M.H. Jr., Klaenhammer T., Richardson P., Kozyavkin S.,
RA   Weimer B.C., Mills D.A.;
RT   "Comparative genomics of the lactic acid bacteria.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:15611-15616(2006).
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.
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; CP000414; ABJ61391.1; -; Genomic_DNA.
DR   RefSeq; WP_011679162.1; NC_008531.1.
DR   PDB; 1EHI; X-ray; 2.38 A; A/B=1-377.
DR   PDBsum; 1EHI; -.
DR   ProteinModelPortal; Q03ZI1; -.
DR   SMR; Q03ZI1; -.
DR   STRING; 203120.LEUM_0264; -.
DR   EnsemblBacteria; ABJ61391; ABJ61391; LEUM_0264.
DR   GeneID; 29575937; -.
DR   KEGG; lme:LEUM_0264; -.
DR   eggNOG; ENOG4105CPF; Bacteria.
DR   eggNOG; COG1181; LUCA.
DR   HOGENOM; HOG000011593; -.
DR   KO; K01921; -.
DR   OMA; YETKYTE; -.
DR   OrthoDB; 764798at2; -.
DR   UniPathway; UPA00219; -.
DR   EvolutionaryTrace; Q03ZI1; -.
DR   Proteomes; UP000000362; Chromosome.
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   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.
FT   CHAIN         1    377       D-alanine--D-alanine ligase.
FT                                /FTId=PRO_1000030463.
FT   DOMAIN      140    349       ATP-grasp. {ECO:0000255|HAMAP-
FT                                Rule:MF_00047}.
FT   NP_BIND     170    225       ATP. {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       303    303       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       316    316       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       316    316       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       318    318       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   STRAND        4     11       {ECO:0000244|PDB:1EHI}.
FT   HELIX        17     34       {ECO:0000244|PDB:1EHI}.
FT   STRAND       35     44       {ECO:0000244|PDB:1EHI}.
FT   HELIX        53     60       {ECO:0000244|PDB:1EHI}.
FT   HELIX        65     73       {ECO:0000244|PDB:1EHI}.
FT   HELIX        86     89       {ECO:0000244|PDB:1EHI}.
FT   STRAND       95    100       {ECO:0000244|PDB:1EHI}.
FT   TURN        104    106       {ECO:0000244|PDB:1EHI}.
FT   STRAND      107    109       {ECO:0000244|PDB:1EHI}.
FT   HELIX       110    117       {ECO:0000244|PDB:1EHI}.
FT   STRAND      122    124       {ECO:0000244|PDB:1EHI}.
FT   HELIX       127    134       {ECO:0000244|PDB:1EHI}.
FT   HELIX       136    144       {ECO:0000244|PDB:1EHI}.
FT   TURN        145    147       {ECO:0000244|PDB:1EHI}.
FT   STRAND      153    156       {ECO:0000244|PDB:1EHI}.
FT   HELIX       160    163       {ECO:0000244|PDB:1EHI}.
FT   HELIX       166    173       {ECO:0000244|PDB:1EHI}.
FT   STRAND      177    183       {ECO:0000244|PDB:1EHI}.
FT   TURN        186    189       {ECO:0000244|PDB:1EHI}.
FT   STRAND      190    193       {ECO:0000244|PDB:1EHI}.
FT   HELIX       196    206       {ECO:0000244|PDB:1EHI}.
FT   TURN        207    209       {ECO:0000244|PDB:1EHI}.
FT   STRAND      213    217       {ECO:0000244|PDB:1EHI}.
FT   STRAND      224    234       {ECO:0000244|PDB:1EHI}.
FT   STRAND      236    244       {ECO:0000244|PDB:1EHI}.
FT   STRAND      248    252       {ECO:0000244|PDB:1EHI}.
FT   HELIX       257    260       {ECO:0000244|PDB:1EHI}.
FT   STRAND      268    272       {ECO:0000244|PDB:1EHI}.
FT   HELIX       277    293       {ECO:0000244|PDB:1EHI}.
FT   STRAND      298    306       {ECO:0000244|PDB:1EHI}.
FT   STRAND      312    320       {ECO:0000244|PDB:1EHI}.
FT   HELIX       328    330       {ECO:0000244|PDB:1EHI}.
FT   HELIX       332    336       {ECO:0000244|PDB:1EHI}.
FT   HELIX       340    360       {ECO:0000244|PDB:1EHI}.
SQ   SEQUENCE   377 AA;  41826 MW;  D1C6A40A6812AE01 CRC64;
     MTKKRVALIF GGNSSEHDVS KRSAQNFYNA IEATGKYEII VFAIAQNGFF LDTESSKKIL
     ALEDEQPIVD AFMKTVDASD PLARIHALKS AGDFDIFFPV VHGNLGEDGT LQGLFKLLDK
     PYVGAPLRGH AVSFDKALTK ELLTVNGIRN TKYIVVDPES ANNWSWDKIV AELGNIVFVK
     AANQGSSVGI SRVTNAEEYT EALSDSFQYD YKVLIEEAVN GARELEVGVI GNDQPLVSEI
     GAHTVPNQGS GDGWYDYNNK FVDNSAVHFE IPAQLSPEVT KEVKQMALDA YKVLNLRGEA
     RMDFLLDENN VPYLGEPNTL PGFTNMSLFK RLWDYSDINN AKLVDMLIDY GFEDFAQNKK
     LSYSFVSLGE EKIGKFN
//
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