ID DDL_NITOC Reviewed; 316 AA. AC Q3J792; DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot. DT 08-NOV-2005, sequence version 1. DT 27-MAR-2024, entry version 109. 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=Noc_2858; OS Nitrosococcus oceani (strain ATCC 19707 / BCRC 17464 / JCM 30415 / NCIMB OS 11848 / C-107). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae; OC Nitrosococcus. OX NCBI_TaxID=323261; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 19707 / BCRC 17464 / JCM 30415 / NCIMB 11848 / C-107; RX PubMed=16957257; DOI=10.1128/aem.00463-06; RA Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J., RA Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T., RA Vergez L.M., Ward B.B.; RT "Complete genome sequence of the marine, chemolithoautotrophic, ammonia- RT oxidizing bacterium Nitrosococcus oceani ATCC 19707."; RL Appl. Environ. Microbiol. 72:6299-6315(2006). 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; CP000127; ABA59304.1; -; Genomic_DNA. DR RefSeq; WP_002812557.1; NC_007484.1. DR AlphaFoldDB; Q3J792; -. DR SMR; Q3J792; -. DR STRING; 323261.Noc_2858; -. DR KEGG; noc:Noc_2858; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_1_2_6; -. DR InParanoid; Q3J792; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000006838; 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:SF23; D-ALANINE--D-ALANINE LIGASE B; 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..316 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_0000341138" FT DOMAIN 109..304 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 135..190 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 258 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 271 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 271 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 273 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" SQ SEQUENCE 316 AA; 34489 MW; 24A361ED8DBEF4CF CRC64; MIGRVDVKAW GKVVVLMGGY SAEREISLKS GTAVLQSLLR QGIEAHGIDV DKGVLTQLSK GQFTRAFIAL HGRGGEDGVI QGVLETLNLP YTGSGVLGSA LTMDKLRSKR LWRGMDLPTA DFSVLTRDTN PALIAADLGL PLIVKPAREG SSLGMMKVES IEALQSAYRE AVIFDTAVFA ERWLPGAEYT AAILADRVLP LIRLETPRVF YDFEAKYHAN TTRYFCPCGL SEKQEQDLQA LALEAFQALG ASGWGRVDLR CDEKAHPYLL EINTVPGMTD HSLVPMAAQA AGIEFDEMVL QILASSLERR MFQDGT //