ID DDL_STRPN Reviewed; 347 AA.
AC P0CB57; O54631;
DT 03-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 03-NOV-2009, sequence version 1.
DT 27-MAR-2024, 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}; Synonyms=ddlA;
GN OrderedLocusNames=SP_1671;
OS Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4).
OC Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=170187;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-334 / TIGR4;
RX PubMed=11463916; DOI=10.1126/science.1061217;
RA Tettelin H., Nelson K.E., Paulsen I.T., Eisen J.A., Read T.D.,
RA Peterson S.N., Heidelberg J.F., DeBoy R.T., Haft D.H., Dodson R.J.,
RA Durkin A.S., Gwinn M.L., Kolonay J.F., Nelson W.C., Peterson J.D.,
RA Umayam L.A., White O., Salzberg S.L., Lewis M.R., Radune D.,
RA Holtzapple E.K., Khouri H.M., Wolf A.M., Utterback T.R., Hansen C.L.,
RA McDonald L.A., Feldblyum T.V., Angiuoli S.V., Dickinson T., Hickey E.K.,
RA Holt I.E., Loftus B.J., Yang F., Smith H.O., Venter J.C., Dougherty B.A.,
RA Morrison D.A., Hollingshead S.K., Fraser C.M.;
RT "Complete genome sequence of a virulent isolate of Streptococcus
RT pneumoniae.";
RL Science 293:498-506(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 155-300.
RA Zhi-Yuan S., Enright M.C., Wilkinson P., Spratt B.G.;
RT "Identification of three major clones of multiply antibiotic resistant
RT Streptococcus pneumoniae in Taiwanese hospitals using multilocus sequence
RT typing.";
RL Submitted (SEP-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 155-301.
RC STRAIN=Various strains;
RA Coffey T.J., Enright M.C., Daniels M., Wilkinson P., Berron S., Fenoll A.,
RA Spratt B.G.;
RT "Recombinational exchanges at the capsular polysaccharide biosynthetic
RT locus lead to frequent serotype changes among natural isolates of
RT Streptococcus pneumoniae.";
RL Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 155-301.
RC STRAIN=Various strains;
RX PubMed=9846740; DOI=10.1099/00221287-144-11-3049;
RA Enright M.C., Spratt B.G.;
RT "A multilocus sequence typing scheme for Streptococcus pneumoniae:
RT identification of clones associated with serious invasive disease.";
RL Microbiology 144:3049-3060(1998).
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; AE005672; AAK75750.1; -; Genomic_DNA.
DR EMBL; AJ233887; CAA13580.1; -; Genomic_DNA.
DR EMBL; Z99894; CAB17019.1; -; Genomic_DNA.
DR EMBL; Z99837; CAB16962.1; -; Genomic_DNA.
DR EMBL; Z99844; CAB16969.1; -; Genomic_DNA.
DR EMBL; Z99845; CAB16970.1; -; Genomic_DNA.
DR EMBL; Z99878; CAB17003.1; -; Genomic_DNA.
DR EMBL; Z99893; CAB17018.1; -; Genomic_DNA.
DR EMBL; AJ232272; CAA13275.1; -; Genomic_DNA.
DR EMBL; AJ232245; CAA13248.1; -; Genomic_DNA.
DR EMBL; AJ232254; CAA13257.1; -; Genomic_DNA.
DR EMBL; AJ232260; CAA13263.1; -; Genomic_DNA.
DR EMBL; AJ232267; CAA13270.1; -; Genomic_DNA.
DR EMBL; AJ232268; CAA13271.1; -; Genomic_DNA.
DR PIR; E95194; E95194.
DR AlphaFoldDB; P0CB57; -.
DR SMR; P0CB57; -.
DR PaxDb; 170187-SP_1671; -.
DR EnsemblBacteria; AAK75750; AAK75750; SP_1671.
DR KEGG; spn:SP_1671; -.
DR eggNOG; COG1181; Bacteria.
DR PhylomeDB; P0CB57; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000000585; 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: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; Cell shape; Cell wall biogenesis/degradation; Cytoplasm;
KW Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Peptidoglycan synthesis; Reference proteome.
FT CHAIN 1..347
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000177887"
FT DOMAIN 131..333
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 161..216
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 287
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 300
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 300
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 302
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT CONFLICT 250
FT /note="K -> N (in Ref. 1; AAK75750)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 347 AA; 38717 MW; AFCF7AB1E53F9289 CRC64;
MKQTIILLYG GRSAEREVSV LSAESVMRAV DYDRFTVKTF FISQSGDFIK TQEFSHAPGQ
EDRLMTNETI DWDKKVAPSA IYEEGAVVFP VLHGPMGEDG SVQGFLEVLK MPYVGCNILS
SSLAMDKITT KRVLESAGIA QVPYVAIVEG DDVTAKIAEV EEKLAYPVFT KPSNMGSSVG
ISKSENQEEL RQALKLAFRY DSRVLVEQGV NAREIEVGLL GNYDVKSTLP GEVVKDVAFY
DYDAKYIDNK ITMDIPAKIS DDVVAVMRQN AETAFRAIGG LGLSRCDFFY TDKGEIFLNE
LNTMPGFTQW SMYPLLWDNM GISYPKLIER LVDLAKESFD KREAHLI
//
