ID DDL_VIBCH Reviewed; 334 AA. AC Q9KM17; DT 02-AUG-2002, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-2000, sequence version 1. DT 27-MAR-2024, entry version 133. 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=VC_A0572; OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; OC Vibrio. OX NCBI_TaxID=243277; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 39315 / El Tor Inaba N16961; RX PubMed=10952301; DOI=10.1038/35020000; RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L., RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R., RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D., RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A., RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L., RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.; RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio RT cholerae."; RL Nature 406:477-483(2000). 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; AE003853; AAF96474.1; -; Genomic_DNA. DR PIR; A82443; A82443. DR RefSeq; NP_232962.1; NC_002506.1. DR RefSeq; WP_000169444.1; NZ_LT906615.1. DR PDB; 6DGI; X-ray; 2.30 A; A/B=1-334. DR PDBsum; 6DGI; -. DR AlphaFoldDB; Q9KM17; -. DR SMR; Q9KM17; -. DR STRING; 243277.VC_A0572; -. DR DNASU; 2612376; -. DR EnsemblBacteria; AAF96474; AAF96474; VC_A0572. DR KEGG; vch:VC_A0572; -. DR PATRIC; fig|243277.26.peg.3199; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_0_0_6; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000000584; Chromosome 2. DR GO; GO:0005829; C:cytosol; IBA:GO_Central. DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW. DR GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IBA:GO_Central. 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; IBA:GO_Central. 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; Reference proteome. FT CHAIN 1..334 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_0000177901" FT DOMAIN 121..327 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 151..206 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 281 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 294 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 294 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 296 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:6DGI" FT HELIX 17..31 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 37..45 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 48..51 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 56..60 FT /evidence="ECO:0007829|PDB:6DGI" FT TURN 61..64 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 65..67 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 72..74 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 76..81 FT /evidence="ECO:0007829|PDB:6DGI" FT TURN 85..90 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 91..99 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 103..105 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 108..115 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 117..126 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 134..137 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 142..155 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 156..162 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 171..174 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 177..179 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 180..188 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 192..198 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 203..212 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 215..218 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 222..225 FT /evidence="ECO:0007829|PDB:6DGI" FT TURN 229..231 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 234..238 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 245..249 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 255..271 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 276..284 FT /evidence="ECO:0007829|PDB:6DGI" FT STRAND 290..298 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 306..313 FT /evidence="ECO:0007829|PDB:6DGI" FT HELIX 318..331 FT /evidence="ECO:0007829|PDB:6DGI" SQ SEQUENCE 334 AA; 37318 MW; B7581B22D766818B CRC64; MTKTTILLLC GGGSSEHEIS LVSANYIQQQ LELTPEFHVI RVEMKKEGWF SEQGALVYLD TNSATLNSDK ASYPIDFVVP CIHGFPGETG DIQSMLELAG IPYLGCGPEA SANSFNKITS KLWYDALDIP NTPYLFLTQN TPSSIDKAKQ AFGHWGSIFV KAARQGSSVG CYKVTTEDQI APAIEAAFGF SEQVLVEQAV KPRELEVSAY EMNGKLYISK PGEVIAPEGT FYSYEEKYSA NSHARTVLEA ENLTEKHKEL IQTYAERVFI HMKLRHLSRI DFFLTQEGQI YLNEVNTFPG MTPISMFPKM LEHNGHRFSE FLVQCVTNTL VNAK //