ID C7QYT8_JONDD Unreviewed; 389 AA. AC C7QYT8; DT 13-OCT-2009, integrated into UniProtKB/TrEMBL. DT 13-OCT-2009, sequence version 1. DT 27-MAR-2024, entry version 86. DE RecName: Full=D-alanine--D-alanine ligase {ECO:0000256|HAMAP-Rule:MF_00047}; DE EC=6.3.2.4 {ECO:0000256|HAMAP-Rule:MF_00047}; DE AltName: Full=D-Ala-D-Ala ligase {ECO:0000256|HAMAP-Rule:MF_00047}; DE AltName: Full=D-alanylalanine synthetase {ECO:0000256|HAMAP-Rule:MF_00047}; GN Name=ddl {ECO:0000256|HAMAP-Rule:MF_00047}; GN OrderedLocusNames=Jden_1680 {ECO:0000313|EMBL:ACV09327.1}; OS Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / BCRC 15368 / CIP OS 55.134 / JCM 11481 / NBRC 15587 / NCTC 10816 / Prevot 55134) (Listeria OS denitrificans). OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Jonesiaceae; OC Jonesia. OX NCBI_TaxID=471856 {ECO:0000313|EMBL:ACV09327.1, ECO:0000313|Proteomes:UP000000628}; RN [1] {ECO:0000313|EMBL:ACV09327.1, ECO:0000313|Proteomes:UP000000628} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 14870 / DSM 20603 / BCRC 15368 / CIP 55.134 / JCM 11481 / RC NBRC 15587 / NCTC 10816 / Prevot 55134 RC {ECO:0000313|Proteomes:UP000000628}; RX PubMed=21304666; DOI=10.4056/sigs.41646; RA Pukall R., Gehrich-Schroter G., Lapidus A., Nolan M., Glavina Del Rio T., RA Lucas S., Chen F., Tice H., Pitluck S., Cheng J.F., Copeland A., RA Saunders E., Brettin T., Detter J.C., Bruce D., Goodwin L., Pati A., RA Ivanova N., Mavromatis K., Ovchinnikova G., Chen A., Palaniappan K., RA Land M., Hauser L., Chang Y.J., Jeffries C.D., Chain P., Goker M., RA Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., RA Klenk H.P., Han C.; RT "Complete genome sequence of Jonesia denitrificans type strain (Prevot RT 55134)."; RL Stand. Genomic Sci. 1:262-269(2009). CC -!- FUNCTION: Cell wall formation. {ECO:0000256|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:0000256|HAMAP-Rule:MF_00047}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; CC Evidence={ECO:0000256|PIRSR:PIRSR039102-3}; CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; CC Evidence={ECO:0000256|PIRSR:PIRSR039102-3}; CC Note=Binds 2 magnesium or manganese ions per subunit. CC {ECO:0000256|PIRSR:PIRSR039102-3}; CC -!- COFACTOR: CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; CC Evidence={ECO:0000256|ARBA:ARBA00001936}; CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis. CC {ECO:0000256|HAMAP-Rule:MF_00047}. CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047}. CC -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family. CC {ECO:0000256|ARBA:ARBA00010871, ECO:0000256|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; CP001706; ACV09327.1; -; Genomic_DNA. DR AlphaFoldDB; C7QYT8; -. DR STRING; 471856.Jden_1680; -. DR KEGG; jde:Jden_1680; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_0_0_11; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000000628; Chromosome. DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell. DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule. 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 {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|PROSITE- KW ProRule:PRU00409}; KW Cell shape {ECO:0000256|ARBA:ARBA00022960, ECO:0000256|HAMAP- KW Rule:MF_00047}; KW Cell wall biogenesis/degradation {ECO:0000256|ARBA:ARBA00023316, KW ECO:0000256|HAMAP-Rule:MF_00047}; KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047}; KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00047}; KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|PIRSR:PIRSR039102-3}; KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|PIRSR:PIRSR039102-3}; KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, KW ECO:0000256|PIRSR:PIRSR039102-3}; KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|PROSITE- KW ProRule:PRU00409}; KW Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984, ECO:0000256|HAMAP- KW Rule:MF_00047}; Reference proteome {ECO:0000313|Proteomes:UP000000628}. FT DOMAIN 168..379 FT /note="ATP-grasp" FT /evidence="ECO:0000259|PROSITE:PS50975" FT BINDING 333 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" FT BINDING 346 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" FT BINDING 346 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" FT BINDING 348 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" SQ SEQUENCE 389 AA; 41494 MW; 26959C787BC7A099 CRC64; MENMSTSQTR PNNLGAPHAA DRVRTRVLVL FGGRSGEHPI SCITAAGVLR AIDRDRFDVV AVGITQGGKW VLASTDPDEV VTSGDDLPHV ADNGTEVLLP FASGDNEVRV IRDGVLESVG PVDVVLPLLH GPFGEDGTVQ GMLELADLRY VGVGVLGSAV GMDKHYMKLV FEGHGLPVGP YTTVFPGQWQ RDPDEVRARV VALGLPVFVK PTRAGSSLGI SKVSDVGDLD RAMAEALKHD PKVIIEAGIV GREIECAVLG GHGDTPARAS LPGEITMTGS AHEFYDFEAK YLDDASAQLS CPAELDETTT ATVREVAVRA FDAVGGEGLS RVDVFVQEDG AVVVNEINTM PGFTPISMYP RMWERSGVSY TELISELIDL ALERPLGLR //