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Database: UniProt/SWISS-PROT
Entry: DDL_PARXL
LinkDB: DDL_PARXL
Original site: DDL_PARXL 
ID   DDL_PARXL               Reviewed;         313 AA.
AC   Q13TZ4;
DT   10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   30-AUG-2017, entry version 87.
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=Bxeno_A3907; ORFNames=Bxe_A0488;
OS   Paraburkholderia xenovorans (strain LB400).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Paraburkholderia.
OX   NCBI_TaxID=266265;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LB400;
RX   PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA   Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA   Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M.,
RA   Lao V., Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A.,
RA   Marx C.J., Parnell J.J., Ramette A., Richardson P., Seeger M.,
RA   Smith D., Spilker T., Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B.,
RA   Tiedje J.M.;
RT   "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp
RT   genome shaped for versatility.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006).
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; CP000270; ABE32445.1; -; Genomic_DNA.
DR   RefSeq; WP_011489915.1; NZ_CP008760.1.
DR   PDB; 4EGJ; X-ray; 2.30 A; A/B/C/D=1-313.
DR   PDBsum; 4EGJ; -.
DR   ProteinModelPortal; Q13TZ4; -.
DR   SMR; Q13TZ4; -.
DR   STRING; 266265.Bxe_A0488; -.
DR   EnsemblBacteria; ABE32445; ABE32445; Bxe_A0488.
DR   GeneID; 4005924; -.
DR   KEGG; bxb:DR64_2664; -.
DR   KEGG; bxe:Bxe_A0488; -.
DR   PATRIC; fig|266265.5.peg.4128; -.
DR   eggNOG; ENOG4105CPF; Bacteria.
DR   eggNOG; COG1181; LUCA.
DR   HOGENOM; HOG000011592; -.
DR   KO; K01921; -.
DR   OMA; YETKYTE; -.
DR   OrthoDB; POG091H00GT; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000001817; Chromosome 1.
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-EC.
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-UniPathway.
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.
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    313       D-alanine--D-alanine ligase.
FT                                /FTId=PRO_0000341080.
FT   DOMAIN      108    308       ATP-grasp. {ECO:0000255|HAMAP-
FT                                Rule:MF_00047}.
FT   NP_BIND     138    193       ATP. {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       262    262       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       275    275       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       275    275       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       277    277       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   HELIX         6      9       {ECO:0000244|PDB:4EGJ}.
FT   STRAND       11     15       {ECO:0000244|PDB:4EGJ}.
FT   HELIX        23     39       {ECO:0000244|PDB:4EGJ}.
FT   STRAND       43     47       {ECO:0000244|PDB:4EGJ}.
FT   TURN         49     51       {ECO:0000244|PDB:4EGJ}.
FT   HELIX        56     59       {ECO:0000244|PDB:4EGJ}.
FT   STRAND       64     67       {ECO:0000244|PDB:4EGJ}.
FT   HELIX        72     74       {ECO:0000244|PDB:4EGJ}.
FT   HELIX        78     86       {ECO:0000244|PDB:4EGJ}.
FT   STRAND       89     92       {ECO:0000244|PDB:4EGJ}.
FT   HELIX        95    101       {ECO:0000244|PDB:4EGJ}.
FT   HELIX       104    113       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      121    125       {ECO:0000244|PDB:4EGJ}.
FT   HELIX       130    141       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      143    149       {ECO:0000244|PDB:4EGJ}.
FT   HELIX       164    166       {ECO:0000244|PDB:4EGJ}.
FT   HELIX       167    174       {ECO:0000244|PDB:4EGJ}.
FT   TURN        175    177       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      179    185       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      189    198       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      206    208       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      228    231       {ECO:0000244|PDB:4EGJ}.
FT   HELIX       236    251       {ECO:0000244|PDB:4EGJ}.
FT   TURN        252    254       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      257    266       {ECO:0000244|PDB:4EGJ}.
FT   STRAND      271    279       {ECO:0000244|PDB:4EGJ}.
FT   HELIX       287    294       {ECO:0000244|PDB:4EGJ}.
FT   HELIX       299    308       {ECO:0000244|PDB:4EGJ}.
SQ   SEQUENCE   313 AA;  33535 MW;  DDBB5D2E458BD6D3 CRC64;
     MSSIDPKQFG KVAVLLGGNS AEREVSLNSG RLVLQGLRDA GIDAHPFDPA ERPLAALKEE
     GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL GLDKFRTKLV WQQLGIPTPP
     FEAVLRGDDY EARAKEIVAK LGLPLFVKPA SEGSSVAVIK VKSADALPAA LIEAVKFDRI
     VVVEKSIEGG GEYTACIAGN LDLPVIRIVP AGEFYDYHAK YIANDTQYLI PCGLTADEEA
     RLKVLARRAF DVLGCTDWGR ADFMLDADGN PYFLEVNTAP GMTDHSLPPK AARAVGISYQ
     ELVVAVLALT LKD
//
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