ID DDL_METI4 Reviewed; 303 AA. AC B3DVV9; DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot. DT 22-JUL-2008, sequence version 1. DT 27-MAR-2024, entry version 91. 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=Minf_1408; OS Methylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain OS V4)). OC Bacteria; Verrucomicrobiota; Methylacidiphilae; Methylacidiphilales; OC Methylacidiphilaceae; Methylacidiphilum (ex Ratnadevi et al. 2023). OX NCBI_TaxID=481448; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=Isolate V4; RX PubMed=18593465; DOI=10.1186/1745-6150-3-26; RA Hou S., Makarova K.S., Saw J.H., Senin P., Ly B.V., Zhou Z., Ren Y., RA Wang J., Galperin M.Y., Omelchenko M.V., Wolf Y.I., Yutin N., Koonin E.V., RA Stott M.B., Mountain B.W., Crowe M.A., Smirnova A.V., Dunfield P.F., RA Feng L., Wang L., Alam M.; RT "Complete genome sequence of the extremely acidophilic methanotroph isolate RT V4, Methylacidiphilum infernorum, a representative of the bacterial phylum RT Verrucomicrobia."; RL Biol. Direct 3:26-26(2008). 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; CP000975; ACD83462.1; -; Genomic_DNA. DR RefSeq; WP_012463744.1; NC_010794.1. DR AlphaFoldDB; B3DVV9; -. DR SMR; B3DVV9; -. DR STRING; 481448.Minf_1408; -. DR KEGG; min:Minf_1408; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_1_1_0; -. DR OrthoDB; 9813261at2; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000009149; 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; 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:SF0; D-ALANINE-D-ALANINE LIGASE FAMILY; 1. DR Pfam; PF07478; Dala_Dala_lig_C; 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; 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. FT CHAIN 1..303 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_1000091194" FT DOMAIN 103..293 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 130..179 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 247 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 260 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 260 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 262 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" SQ SEQUENCE 303 AA; 33194 MW; 4B0BC4D8738D0BEA CRC64; MNPALPRHIA VLKGGPSEER EISLRTAKAV EDALSSLGYE ISSIDVTTEK FEIPRDAEIC FLCIHGSFGE DGQIQRLLMR RGIPFTGSDA SSSEKAFDKA WSKTLFIKGG IPTPPFCVVG DGKKIPFDPP YVIKPSRQGS SIGIEFVYDI KELDQAIKKS TQYDHVVLAE ALITGKELTV GILDGKALPV VEIKPKEGFY DYHHKYTKGA STYFCPAPLT VDQTSAVQKT ALDAFNVLGC SVYGRVDIIL SDNGIPWVLE INTIPGMTET SLFPMAAKAS GMNFAQLCEK ILEISYLRWK AHG //