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Database: UniProt/SWISS-PROT
Entry: DDL_PEDPA
LinkDB: DDL_PEDPA
Original site: DDL_PEDPA 
ID   DDL_PEDPA               Reviewed;         351 AA.
AC   Q03EM9;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   14-NOV-2006, sequence version 1.
DT   27-SEP-2017, entry version 73.
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=PEPE_1302;
OS   Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 /
OS   183-1w).
OC   Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae;
OC   Pediococcus.
OX   NCBI_TaxID=278197;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w;
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: 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; CP000422; ABJ68343.1; -; Genomic_DNA.
DR   RefSeq; WP_002833700.1; NC_008525.1.
DR   ProteinModelPortal; Q03EM9; -.
DR   SMR; Q03EM9; -.
DR   STRING; 278197.PEPE_1302; -.
DR   EnsemblBacteria; ABJ68343; ABJ68343; PEPE_1302.
DR   GeneID; 33061559; -.
DR   KEGG; ppe:PEPE_1302; -.
DR   eggNOG; ENOG4105CPF; Bacteria.
DR   eggNOG; COG1181; LUCA.
DR   HOGENOM; HOG000011592; -.
DR   OMA; MQGLLEC; -.
DR   OrthoDB; POG091H00GT; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000000773; 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-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.
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    351       D-alanine--D-alanine ligase.
FT                                /FTId=PRO_1000030476.
FT   DOMAIN      146    340       ATP-grasp. {ECO:0000255|HAMAP-
FT                                Rule:MF_00047}.
FT   NP_BIND     173    226       ATP. {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       295    295       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       307    307       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       307    307       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       309    309       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
SQ   SEQUENCE   351 AA;  38351 MW;  DB5C222F9E3FFE6C CRC64;
     MKIAVLAGGK STERNVSLSS GSKITNALRS KGYDATMIDL FLGYELEDGQ SYEDVFKSSN
     TSTDYEISDA VLTEEDIEEL RTDGTVGLFG KNVLPILQAA DFVFLALHGG DGENGKVQAV
     LDLNHIKYTG SGSLASGIAM DKAISKEIML YNNIKTAQFA VLHAKDGIHP QLAFDYPMVV
     KPNSGGSSIG TRIVHDEAEL AESLKDAYRF DDEIIVEEFI TGREFSLGVV NGQAMPAIEI
     VVNDGWYDYE HKFQTGSTTK FVTPPEIEDD VHDEMKRVAV QTMDALGMTN YGRVDFLTND
     TGVYVIEANN LPGMTPLSLL PQEAEAAGIS YEDLCESIVL GKQKLYDELK K
//
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