DDL_STRMU
ID DDL_STRMU Reviewed; 349 AA.
AC P95803;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 28-NOV-2002, sequence version 2.
DT 03-AUG-2022, entry version 142.
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}; OrderedLocusNames=SMU_599;
OS Streptococcus mutans serotype c (strain ATCC 700610 / UA159).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=210007;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700610 / UA159;
RX PubMed=12397186; DOI=10.1073/pnas.172501299;
RA Ajdic D.J., McShan W.M., McLaughlin R.E., Savic G., Chang J., Carson M.B.,
RA Primeaux C., Tian R., Kenton S., Jia H.G., Lin S.P., Qian Y., Li S.,
RA Zhu H., Najar F.Z., Lai H., White J., Roe B.A., Ferretti J.J.;
RT "Genome sequence of Streptococcus mutans UA159, a cariogenic dental
RT pathogen.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:14434-14439(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 106-303.
RC STRAIN=ATCC 25175 / DSM 20523 / JCM 5705 / NBRC 13955 / NCIMB 702062 / NCTC
RC 10449;
RA Garnier F., Gerbaud G., Courvalin P., Galimand M.;
RL Submitted (FEB-1997) 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; AE014133; AAN58338.1; -; Genomic_DNA.
DR EMBL; U69165; AAB41854.1; -; Genomic_DNA.
DR RefSeq; NP_721032.1; NC_004350.2.
DR RefSeq; WP_002352219.1; NC_004350.2.
DR PDB; 3K3P; X-ray; 2.23 A; A/B=1-349.
DR PDBsum; 3K3P; -.
DR AlphaFoldDB; P95803; -.
DR SMR; P95803; -.
DR STRING; 210007.SMU_599; -.
DR PRIDE; P95803; -.
DR EnsemblBacteria; AAN58338; AAN58338; SMU_599.
DR KEGG; smu:SMU_599; -.
DR PATRIC; fig|210007.7.peg.532; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_9; -.
DR OMA; NTTPGMT; -.
DR PhylomeDB; P95803; -.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; P95803; -.
DR Proteomes; UP000002512; 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..349
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000177886"
FT DOMAIN 133..335
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 163..218
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 289
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 302
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
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 BINDING 304
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT CONFLICT 132
FT /note="N -> K (in Ref. 2; AAB41854)"
FT /evidence="ECO:0000305"
FT CONFLICT 238
FT /note="D -> V (in Ref. 2; AAB41854)"
FT /evidence="ECO:0000305"
FT CONFLICT 273
FT /note="A -> R (in Ref. 2; AAB41854)"
FT /evidence="ECO:0000305"
FT STRAND 4..11
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 17..30
FT /evidence="ECO:0007829|PDB:3K3P"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 49..57
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 79..82
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 88..92
FT /evidence="ECO:0007829|PDB:3K3P"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 99..101
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 102..109
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 119..126
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 128..138
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 146..150
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 155..165
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 168..174
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 184..188
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 189..202
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 204..210
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 214..226
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 233..235
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 263..279
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 284..292
FT /evidence="ECO:0007829|PDB:3K3P"
FT STRAND 298..306
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 314..321
FT /evidence="ECO:0007829|PDB:3K3P"
FT HELIX 326..345
FT /evidence="ECO:0007829|PDB:3K3P"
SQ SEQUENCE 349 AA; 38838 MW; FFDAAD9942CAE7EF CRC64;
MSKETLVLLY GGRSAERDVS VLSAESVMRA INYDNFLVKT YFITQAGDFI KTQEFDSQPS
ETDKLMTNDT IIASQKIKPS DIYEEEAVVF PVLHGPMGED GSIQGFLEVL KMPYVGTNIL
SSSVAMDKIT TNQVLESATT IPQVAYVALI EGEPLESKLA EVEEKLIYPV FVKPANMGSS
VGISKAENRT DLKQAIALAL KYDSRVLIEQ GVDAREIEVG ILGNTDVKTT LPGEIVKDVA
FYDYEAKYID NKITMAIPAE IDPVIVEKMR DYAATAFRTL GCCGLSRCDF FLTEDGKVYL
NELNTMPGFT QWSMYPLLWE NMGLSYSVLI EELVSLAKEM FDKRESHLV
