ID DDL_RUEPO Reviewed; 306 AA. AC Q5LU57; DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot. DT 01-FEB-2005, 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}; OrderedLocusNames=SPO1201; OS Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter OS pomeroyi). OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; OC Roseobacteraceae; Ruegeria. OX NCBI_TaxID=246200; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3; RX PubMed=15602564; DOI=10.1038/nature03170; RA Moran M.A., Buchan A., Gonzalez J.M., Heidelberg J.F., Whitman W.B., RA Kiene R.P., Henriksen J.R., King G.M., Belas R., Fuqua C., Brinkac L.M., RA Lewis M., Johri S., Weaver B., Pai G., Eisen J.A., Rahe E., Sheldon W.M., RA Ye W., Miller T.R., Carlton J., Rasko D.A., Paulsen I.T., Ren Q., RA Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R., RA Nelson W.C., Sullivan S.A., Rosovitz M.J., Haft D.H., Selengut J., Ward N.; RT "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine RT environment."; RL Nature 432:910-913(2004). RN [2] RP GENOME REANNOTATION. RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3; RX PubMed=25780504; DOI=10.1186/1944-3277-9-11; RA Rivers A.R., Smith C.B., Moran M.A.; RT "An updated genome annotation for the model marine bacterium Ruegeria RT pomeroyi DSS-3."; RL Stand. Genomic Sci. 9:11-11(2014). 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; CP000031; AAV94497.1; -; Genomic_DNA. DR AlphaFoldDB; Q5LU57; -. DR SMR; Q5LU57; -. DR STRING; 246200.SPO1201; -. DR PaxDb; 246200-SPO1201; -. DR KEGG; sil:SPO1201; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_1_1_5; -. DR OrthoDB; 9813261at2; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000001023; 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:SF0; D-ALANINE-D-ALANINE LIGASE FAMILY; 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..306 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_0000341173" FT DOMAIN 107..300 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 134..184 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 251 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 267 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 267 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 269 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" SQ SEQUENCE 306 AA; 32716 MW; F7056B1A09A3675B CRC64; MGMSSRTNPK VAVLMGGPSA EREVSLVSGR ECAAALRGEG FEVVELDAGS DLCDRLRASA PDVVFNALHG RWGEDGCVQG LLEWLRIPYT SSGVLASALA MDKERSKEAY RAAGLPVAAS QLADRAAIEA AHVMQPPYVV KPYNEGSSVG VYIVTEAANG PPVLAPDLPA TLMVEEYVPG RELSTTVLGD RALNVTDIIT DGWYDYHAKY SPGGSRHVIP ADLPPEIFEL CLDYALRAHK ALGCRGLSRT DFRWDESRGA AGLFLLETNT QPGMTPTSLA PEQALAAGMS FGQLCAWMVE DASCDR //