ID   DDL_BACAN               Reviewed;         304 AA.
AC   Q81Q29; Q6HY93; Q6KY66;
DT   15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2003, sequence version 1.
DT   27-MAR-2024, entry version 144.
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}; Synonyms=ddlB;
GN   OrderedLocusNames=BA_2610, GBAA_2610, BAS2435;
OS   Bacillus anthracis.
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC   Bacillus cereus group.
OX   NCBI_TaxID=1392;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Ames / isolate Porton;
RX   PubMed=12721629; DOI=10.1038/nature01586;
RA   Read T.D., Peterson S.N., Tourasse N.J., Baillie L.W., Paulsen I.T.,
RA   Nelson K.E., Tettelin H., Fouts D.E., Eisen J.A., Gill S.R.,
RA   Holtzapple E.K., Okstad O.A., Helgason E., Rilstone J., Wu M.,
RA   Kolonay J.F., Beanan M.J., Dodson R.J., Brinkac L.M., Gwinn M.L.,
RA   DeBoy R.T., Madpu R., Daugherty S.C., Durkin A.S., Haft D.H., Nelson W.C.,
RA   Peterson J.D., Pop M., Khouri H.M., Radune D., Benton J.L., Mahamoud Y.,
RA   Jiang L., Hance I.R., Weidman J.F., Berry K.J., Plaut R.D., Wolf A.M.,
RA   Watkins K.L., Nierman W.C., Hazen A., Cline R.T., Redmond C., Thwaite J.E.,
RA   White O., Salzberg S.L., Thomason B., Friedlander A.M., Koehler T.M.,
RA   Hanna P.C., Kolstoe A.-B., Fraser C.M.;
RT   "The genome sequence of Bacillus anthracis Ames and comparison to closely
RT   related bacteria.";
RL   Nature 423:81-86(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Ames ancestor;
RX   PubMed=18952800; DOI=10.1128/jb.01347-08;
RA   Ravel J., Jiang L., Stanley S.T., Wilson M.R., Decker R.S., Read T.D.,
RA   Worsham P., Keim P.S., Salzberg S.L., Fraser-Liggett C.M., Rasko D.A.;
RT   "The complete genome sequence of Bacillus anthracis Ames 'Ancestor'.";
RL   J. Bacteriol. 191:445-446(2009).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Sterne;
RA   Brettin T.S., Bruce D., Challacombe J.F., Gilna P., Han C., Hill K.,
RA   Hitchcock P., Jackson P., Keim P., Longmire J., Lucas S., Okinaka R.,
RA   Richardson P., Rubin E., Tice H.;
RT   "Complete genome sequence of Bacillus anthracis Sterne.";
RL   Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
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. {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}.
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DR   EMBL; AE016879; AAP26458.1; -; Genomic_DNA.
DR   EMBL; AE017334; AAT31727.1; -; Genomic_DNA.
DR   EMBL; AE017225; AAT54746.1; -; Genomic_DNA.
DR   RefSeq; NP_844972.1; NC_003997.3.
DR   RefSeq; WP_003157623.1; NZ_WXXI01000021.1.
DR   RefSeq; YP_028695.1; NC_005945.1.
DR   PDB; 3R23; X-ray; 2.50 A; A/B=1-304.
DR   PDB; 3R5X; X-ray; 2.00 A; A/B/C/D=1-304.
DR   PDBsum; 3R23; -.
DR   PDBsum; 3R5X; -.
DR   AlphaFoldDB; Q81Q29; -.
DR   SMR; Q81Q29; -.
DR   STRING; 261594.GBAA_2610; -.
DR   DNASU; 1086552; -.
DR   GeneID; 45022466; -.
DR   KEGG; ban:BA_2610; -.
DR   KEGG; bar:GBAA_2610; -.
DR   KEGG; bat:BAS2435; -.
DR   PATRIC; fig|198094.11.peg.2589; -.
DR   eggNOG; COG1181; Bacteria.
DR   HOGENOM; CLU_039268_1_1_9; -.
DR   OMA; NMHSKYF; -.
DR   OrthoDB; 9813261at2; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000000427; Chromosome.
DR   Proteomes; UP000000594; 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; 3.40.50.20; -; 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:SF0; D-ALANINE-D-ALANINE LIGASE FAMILY; 1.
DR   Pfam; PF07478; Dala_Dala_lig_C; 1.
DR   Pfam; PF01820; Dala_Dala_lig_N; 2.
DR   PIRSF; PIRSF039102; Ddl/VanB; 1.
DR   SMART; SM01209; GARS_A; 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   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation;
KW   Cytoplasm; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW   Peptidoglycan synthesis; Reference proteome.
FT   CHAIN           1..304
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_0000177781"
FT   DOMAIN          99..293
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         126..181
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         248
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         260
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         260
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         262
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   STRAND          1..7
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           11..27
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   TURN            30..32
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          33..39
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           43..45
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           46..49
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   TURN            50..52
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          54..58
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           63..66
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           69..77
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          81..84
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           86..93
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           95..104
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          112..119
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           123..129
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          131..137
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          142..144
FT                   /evidence="ECO:0007829|PDB:3R23"
FT   STRAND          147..149
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           152..165
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          167..173
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          177..185
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          193..202
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          205..217
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           222..238
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          243..252
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   STRAND          255..264
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           272..279
FT                   /evidence="ECO:0007829|PDB:3R5X"
FT   HELIX           284..302
FT                   /evidence="ECO:0007829|PDB:3R5X"
SQ   SEQUENCE   304 AA;  33852 MW;  FB85F1B59BC2B9B2 CRC64;
     MRIGVIMGGV SSEKQVSIMT GNEMIANLDK NKYEIVPITL NEKMDLIEKA KDIDFALLAL
     HGKYGEDGTV QGTLESLGIP YSGSNMLSSG ICMDKNISKK ILRYEGIETP DWIELTKMED
     LNFDELDKLG FPLVVKPNSG GSSVGVKIVY DKDELISMLE TVFEWDSEVV IEKYIKGEEI
     TCSIFDGKQL PIISIRHAAE FFDYNAKYDD ASTIEEVIEL PAELKERVNK ASLACYKALK
     CSVYARVDMM VKDGIPYVME VNTLPGMTQA SLLPKSADAA GIHYSKLLDM IIETSLRVRK
     EEGF
//