GenomeNet

Database: UniProt/TrEMBL
Entry: D4G5D4_BACNB
LinkDB: D4G5D4_BACNB
Original site: D4G5D4_BACNB 
ID   D4G5D4_BACNB            Unreviewed;       354 AA.
AC   D4G5D4;
DT   18-MAY-2010, integrated into UniProtKB/TrEMBL.
DT   03-SEP-2014, sequence version 2.
DT   24-JAN-2024, entry version 72.
DE   RecName: Full=D-alanine--D-alanine ligase {ECO:0000256|HAMAP-Rule:MF_00047};
DE            EC=6.3.2.4 {ECO:0000256|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-Ala-D-Ala ligase {ECO:0000256|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-alanylalanine synthetase {ECO:0000256|HAMAP-Rule:MF_00047};
GN   Name=ddl {ECO:0000256|HAMAP-Rule:MF_00047,
GN   ECO:0000313|EMBL:BAI83940.2};
GN   ORFNames=BSNT_06801 {ECO:0000313|EMBL:BAI83940.2};
OS   Bacillus subtilis subsp. natto (strain BEST195).
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=645657 {ECO:0000313|EMBL:BAI83940.2, ECO:0000313|Proteomes:UP000006805};
RN   [1] {ECO:0000313|EMBL:BAI83940.2, ECO:0000313|Proteomes:UP000006805}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=BEST195 {ECO:0000313|EMBL:BAI83940.2,
RC   ECO:0000313|Proteomes:UP000006805};
RX   PubMed=20398357; DOI=10.1186/1471-2164-11-243;
RA   Nishito Y., Osana Y., Hachiya T., Popendorf K., Toyoda A., Fujiyama A.,
RA   Itaya M., Sakakibara Y.;
RT   "Whole genome assembly of a natto production strain Bacillus subtilis natto
RT   from very short read data.";
RL   BMC Genomics 11:243-243(2010).
RN   [2] {ECO:0000313|EMBL:BAI83940.2, ECO:0000313|Proteomes:UP000006805}
RP   GENOME REANNOTATION.
RC   STRAIN=BEST195 {ECO:0000313|EMBL:BAI83940.2,
RC   ECO:0000313|Proteomes:UP000006805};
RX   PubMed=25329997; DOI=10.1371/journal.pone.0109999;
RA   Kamada M., Hase S., Sato K., Toyoda A., Fujiyama A., Sakakibara Y.;
RT   "Whole genome complete resequencing of Bacillus subtilis natto by combining
RT   long reads with high-quality short reads.";
RL   PLoS ONE 9:E109999-E109999(2014).
CC   -!- FUNCTION: Cell wall formation. {ECO:0000256|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:0000256|HAMAP-Rule:MF_00047};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
CC       Note=Binds 2 magnesium or manganese ions per subunit.
CC       {ECO:0000256|PIRSR:PIRSR039102-3};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|ARBA:ARBA00001936};
CC   -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC       {ECO:0000256|HAMAP-Rule:MF_00047}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047}.
CC   -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC       {ECO:0000256|ARBA:ARBA00010871, ECO:0000256|HAMAP-Rule:MF_00047}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AP011541; BAI83940.2; -; Genomic_DNA.
DR   AlphaFoldDB; D4G5D4; -.
DR   STRING; 86029.AWV81_02575; -.
DR   KEGG; bso:BSNT_06801; -.
DR   HOGENOM; CLU_039268_0_0_9; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000006805; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
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; 3.40.50.20; -; 1.
DR   Gene3D; 3.30.1490.20; ATP-grasp fold, A domain; 1.
DR   Gene3D; 3.30.470.20; ATP-grasp fold, B domain; 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   NCBIfam; TIGR01205; D_ala_D_alaTIGR; 1.
DR   PANTHER; PTHR23132; D-ALANINE--D-ALANINE LIGASE; 1.
DR   PANTHER; PTHR23132:SF25; D-ALANINE--D-ALANINE LIGASE A; 1.
DR   Pfam; PF07478; Dala_Dala_lig_C; 1.
DR   Pfam; PF01820; Dala_Dala_lig_N; 1.
DR   PIRSF; PIRSF039102; Ddl/VanB; 1.
DR   SUPFAM; SSF56059; Glutathione synthetase ATP-binding domain-like; 1.
DR   SUPFAM; SSF52440; PreATP-grasp domain; 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 {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|PROSITE-
KW   ProRule:PRU00409};
KW   Cell shape {ECO:0000256|ARBA:ARBA00022960, ECO:0000256|HAMAP-
KW   Rule:MF_00047};
KW   Cell wall biogenesis/degradation {ECO:0000256|ARBA:ARBA00023316,
KW   ECO:0000256|HAMAP-Rule:MF_00047};
KW   Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00047};
KW   Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|PIRSR:PIRSR039102-3};
KW   Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|PIRSR:PIRSR039102-3};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW   ECO:0000256|PIRSR:PIRSR039102-3};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|PROSITE-
KW   ProRule:PRU00409};
KW   Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984, ECO:0000256|HAMAP-
KW   Rule:MF_00047}.
FT   DOMAIN          133..338
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000259|PROSITE:PS50975"
FT   BINDING         292
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         305
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         305
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         307
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
SQ   SEQUENCE   354 AA;  39102 MW;  7DEFEDC555025FC0 CRC64;
     MYGGKSAEHN VSLQTALAVI KALNTEKFDI HPIYITEKGE WVRGARLTEP VSNVKMLQFE
     QGGSAFSPAA LNQEMFPQEA SQQNEAIDVV FPLLHGPNGE DGTIQGMLEL LNIPYVGNGV
     LASSAGMDKV VMKHLFAQAG LAQAKYAAFL KKDWTRSPKE SCEQVEQELG YPCFVKPANL
     GSSVGISKCR NREELQKAFE LAFQYDRKVV VEEGINGREI EIGVLGNDDP KCSVVGEIAP
     KTDFYDYKAK YEDGDTDLMI PAIVTDEEYA TISDMAIKAF KAIDGSGLVR ADFFLTADGE
     VLINEVNTMP GFTPFSMFPL LWKEAGVEYA DLIEQLVELA KERHAEKQLI KHTF
//
DBGET integrated database retrieval system