ID DDL_NOCFA Reviewed; 363 AA. AC Q5YRY7; DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot. DT 23-NOV-2004, sequence version 1. DT 27-MAR-2024, entry version 116. 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=NFA_42050; OS Nocardia farcinica (strain IFM 10152). OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae; OC Nocardia. OX NCBI_TaxID=247156; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=IFM 10152; RX PubMed=15466710; DOI=10.1073/pnas.0406410101; RA Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K., RA Shiba T., Hattori M.; RT "The complete genomic sequence of Nocardia farcinica IFM 10152."; RL Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004). 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; AP006618; BAD59054.1; -; Genomic_DNA. DR RefSeq; WP_011210739.1; NC_006361.1. DR AlphaFoldDB; Q5YRY7; -. DR SMR; Q5YRY7; -. DR STRING; 247156.NFA_42050; -. DR GeneID; 61134839; -. DR KEGG; nfa:NFA_42050; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_0_1_11; -. DR OrthoDB; 9813261at2; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000006820; 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 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; Reference proteome. FT CHAIN 1..363 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_0000341140" FT DOMAIN 148..353 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 176..231 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 308 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 320 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 320 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 322 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" SQ SEQUENCE 363 AA; 38228 MW; EB08DE40900C2449 CRC64; MTNRIRVAVV FGGRSNEHAV SCVSAGSVLR HLDPTRYEAV PIGITPQGGW VLANSDVAAI GLSHEALPSV DAGGTALTLT ADPTRGGELV ALDDAGAVLG TVDVVFPILH GPFGEDGTLQ GMLELAGVPY VGPGVLASAA GMDKEFTKKL LAAEGLPVGT QVVLRPGTAT LTEEQRERLG LPVFVKPARA GSSIGITKVD DWAALDTAIA AAREHDPKVI VEAGIVGREV ECGVLEFPDG RISASVLAEI RMPEGDGPQF YDFDTKYLDD VCEFDVPAKL DDDIAEQVRE LAVRAFQALD CQGLARVDFF VTADGPVINE INTMPGFTSI SMYPRMWEAT GIDYGTLVST LIETALARGT GLR //