DDL_STAAC
ID DDL_STAAC Reviewed; 356 AA.
AC Q5HEB7;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 113.
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=SACOL2074;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
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; CP000046; AAW37036.1; -; Genomic_DNA.
DR RefSeq; WP_000159631.1; NC_002951.2.
DR PDB; 2I80; X-ray; 2.19 A; A/B=1-356.
DR PDB; 2I87; X-ray; 2.00 A; A/B=1-356.
DR PDB; 2I8C; X-ray; 2.46 A; A/B=1-356.
DR PDB; 3N8D; X-ray; 2.30 A; A/B=1-356.
DR PDBsum; 2I80; -.
DR PDBsum; 2I87; -.
DR PDBsum; 2I8C; -.
DR PDBsum; 3N8D; -.
DR AlphaFoldDB; Q5HEB7; -.
DR SMR; Q5HEB7; -.
DR DrugBank; DB07805; 3-CHLORO-2,2-DIMETHYL-N-[4-(TRIFLUOROMETHYL)PHENYL]PROPANAMIDE.
DR EnsemblBacteria; AAW37036; AAW37036; SACOL2074.
DR KEGG; sac:SACOL2074; -.
DR HOGENOM; CLU_039268_0_0_9; -.
DR OMA; NTTPGMT; -.
DR BioCyc; MetaCyc:MON-15463; -.
DR BRENDA; 6.3.2.4; 3352.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; Q5HEB7; -.
DR Proteomes; UP000000530; 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.
FT CHAIN 1..356
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000177874"
FT DOMAIN 134..339
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 167..222
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 293
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 306
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 306
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 308
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT STRAND 4..11
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 17..29
FT /evidence="ECO:0007829|PDB:2I87"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 70..73
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 77..80
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 85..87
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 104..112
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 121..128
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 130..140
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 147..151
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 152..169
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 172..180
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 182..184
FT /evidence="ECO:0007829|PDB:3N8D"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 193..204
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 208..214
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 219..230
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 267..283
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 288..296
FT /evidence="ECO:0007829|PDB:2I87"
FT STRAND 302..310
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 318..325
FT /evidence="ECO:0007829|PDB:2I87"
FT HELIX 330..356
FT /evidence="ECO:0007829|PDB:2I87"
SQ SEQUENCE 356 AA; 40231 MW; 65822883958DC645 CRC64;
MTKENICIVF GGKSAEHEVS ILTAQNVLNA IDKDKYHVDI IYITNDGDWR KQNNITAEIK
STDELHLENG EALEISQLLK ESSSGQPYDA VFPLLHGPNG EDGTIQGLFE VLDVPYVGNG
VLSAASSMDK LVMKQLFEHR GLPQLPYISF LRSEYEKYEH NILKLVNDKL NYPVFVKPAN
LGSSVGISKC NNEAELKEGI KEAFQFDRKL VIEQGVNARE IEVAVLGNDY PEATWPGEVV
KDVAFYDYKS KYKDGKVQLQ IPADLDEDVQ LTLRNMALEA FKATDCSGLV RADFFVTEDN
QIYINETNAM PGFTAFSMYP KLWENMGLSY PELITKLIEL AKERHQDKQK NKYKID
