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 27-MAR-2024, entry version 119. 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}; GN OrderedLocusNames=SACOL2074; OS Staphylococcus aureus (strain COL). OC Bacteria; Bacillota; 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 KEGG; sac:SACOL2074; -. DR HOGENOM; CLU_039268_0_0_9; -. DR BioCyc; MetaCyc:MONOMER-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; 3.40.50.20; -; 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 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 //