DDL_BACAN
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 03-AUG-2022, entry version 138.
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; Firmicutes; 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; 260799.BAS2435; -.
DR DNASU; 1086552; -.
DR EnsemblBacteria; AAP26458; AAP26458; BA_2610.
DR EnsemblBacteria; AAT31727; AAT31727; GBAA_2610.
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; MQGLLEC; -.
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; 3.30.1490.20; -; 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; 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
