ID DDLB_BRADU Reviewed; 376 AA. AC Q89PS5; DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot. DT 01-JUN-2003, sequence version 1. DT 27-MAR-2024, entry version 119. DE RecName: Full=D-alanine--D-alanine ligase B {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 B {ECO:0000255|HAMAP-Rule:MF_00047}; DE AltName: Full=D-alanylalanine synthetase B {ECO:0000255|HAMAP-Rule:MF_00047}; GN Name=ddlA {ECO:0000255|HAMAP-Rule:MF_00047}; Synonyms=ddlB; GN OrderedLocusNames=blr3405; OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / OS NBRC 14792 / USDA 110). OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; OC Nitrobacteraceae; Bradyrhizobium. OX NCBI_TaxID=224911; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110; RX PubMed=12597275; DOI=10.1093/dnares/9.6.189; RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.; RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium RT Bradyrhizobium japonicum USDA110."; RL DNA Res. 9:189-197(2002). 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; BA000040; BAC48670.1; -; Genomic_DNA. DR RefSeq; NP_770045.1; NC_004463.1. DR AlphaFoldDB; Q89PS5; -. DR SMR; Q89PS5; -. DR STRING; 224911.AAV28_14055; -. DR EnsemblBacteria; BAC48670; BAC48670; BAC48670. DR KEGG; bja:blr3405; -. DR PATRIC; fig|224911.5.peg.3409; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_0_0_5; -. DR InParanoid; Q89PS5; -. DR OrthoDB; 9813261at2; -. DR PhylomeDB; Q89PS5; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000002526; Chromosome. 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 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..376 FT /note="D-alanine--D-alanine ligase B" FT /id="PRO_0000177793" FT DOMAIN 155..361 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 184..239 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 316 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 328 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 328 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 330 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" SQ SEQUENCE 376 AA; 39991 MW; ADF689A391337460 CRC64; MTAYGGEMTK ERRKITVGLL FGGRSAEHEV SRASAANILR ALNSDRYDVY LIGISRDGRW FACDSGNGAG TGSTALTISD EAPEIGLVPG GRGRLVHCDG PTGSDAGSID VAFPILHGPN GEDGTVQGAL ELADVSFVGS SVTGSAVAMD KEVSKRLMRD AGLPVVPFLT TTASSRIEYA AAVAALGTPD LFVKPANLGS SVGVSRARSE EEFAASCALA FRYDRKILVE QALNGAREIE CSVLEESTGD IRASGLGEIV RASEHGFYSY QAKYIDADGA ALHIPADLPL LQARRLQELA VEVFNVLCCE GMARVDFFVQ GDEVFVNEAN TLPGFTSSSM YPKLWEASGL SQTDLMDKLI AHAFARHERR RALSFG //