ID D3PM04_MEIRD Unreviewed; 322 AA. AC D3PM04; DT 20-APR-2010, integrated into UniProtKB/TrEMBL. DT 20-APR-2010, sequence version 1. DT 27-MAR-2024, entry version 90. 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 ECO:0000313|EMBL:AGK03569.1}; GN OrderedLocusNames=Mrub_0337 {ECO:0000313|EMBL:ADD27115.1}; GN ORFNames=K649_01305 {ECO:0000313|EMBL:AGK03569.1}; OS Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus OS ruber). OC Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Meiothermus. OX NCBI_TaxID=504728 {ECO:0000313|EMBL:AGK03569.1, ECO:0000313|Proteomes:UP000013026}; RN [1] {ECO:0000313|EMBL:ADD27115.1, ECO:0000313|Proteomes:UP000006655} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 35948 / DSM 1279 / VKM B-1258 / 21 RC {ECO:0000313|Proteomes:UP000006655}, and DSM 1279 RC {ECO:0000313|EMBL:ADD27115.1}; RX PubMed=21304689; DOI=10.4056/sigs.1032748; RA Tindall B.J., Sikorski J., Lucas S., Goltsman E., Copeland A., RA Glavina Del Rio T., Nolan M., Tice H., Cheng J.F., Han C., Pitluck S., RA Liolios K., Ivanova N., Mavromatis K., Ovchinnikova G., Pati A., RA Fahnrich R., Goodwin L., Chen A., Palaniappan K., Land M., Hauser L., RA Chang Y.J., Jeffries C.D., Rohde M., Goker M., Woyke T., Bristow J., RA Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., RA Lapidus A.; RT "Complete genome sequence of Meiothermus ruber type strain (21)."; RL Stand. Genomic Sci. 3:26-36(2010). RN [2] {ECO:0000313|EMBL:AGK03569.1} RP NUCLEOTIDE SEQUENCE. RC STRAIN=DSM 1279 {ECO:0000313|EMBL:AGK03569.1}; RA Klammer A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., RA Eichler E., Turner S.W.; RT "Non-Hybrid, Finished Microbial Genome Assemblies from Long-Read SMRT RT Sequencing Data."; RL Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases. RN [3] {ECO:0000313|EMBL:AGK03569.1, ECO:0000313|Proteomes:UP000013026} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 35948 / DSM 1279 / VKM B-1258 / 21 RC {ECO:0000313|Proteomes:UP000013026}, and DSM 1279 RC {ECO:0000313|EMBL:AGK03569.1}; RA Chin J., Alexander D.H., Marks P., Korlach J., Clum A., Copeland A.; RL Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases. 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; CP001743; ADD27115.1; -; Genomic_DNA. DR EMBL; CP005385; AGK03569.1; -; Genomic_DNA. DR RefSeq; WP_013012634.1; NC_021081.1. DR AlphaFoldDB; D3PM04; -. DR STRING; 504728.K649_01305; -. DR KEGG; mrb:Mrub_0337; -. DR KEGG; mre:K649_01305; -. DR PATRIC; fig|504728.9.peg.271; -. DR eggNOG; COG1181; Bacteria. DR OrthoDB; 9813261at2; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000006655; Chromosome. DR Proteomes; UP000013026; 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. 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}. FT DOMAIN 120..317 FT /note="ATP-grasp" FT /evidence="ECO:0000259|PROSITE:PS50975" FT BINDING 271 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" FT BINDING 284 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" FT BINDING 284 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" FT BINDING 286 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3" SQ SEQUENCE 322 AA; 35231 MW; 396C70BD2892732B CRC64; MKVLLLAGGP PGEHEVSLSS ARGVLAAMPH PTELVVIAKD GRWLLGEDAY EALRAGVAEQ GTHPFPPPVP WQHYDVVFPL LHGPLGEDGV IQGFLQLLRR PYVGAGVASS ALCMDKDLCK RVLRQAGIPV VPWVTLYKGE PTPQPPFPPP YFVKPANTGS SVGISKVKAD QDATRALAEA FAWDDKVLVE QGIEGVRELE VALLGNIHAE ASVVGEITYQ SEFYDYETKY TEGKAQLHLP APIPPELSDE IRATALEAYR ILGVRGMARV DFFLSPQGEL YLNEFNTIPG FTPTSMYPKL WQATGLAYPD LLDRLVRLAL ER //