ID DDL_COXBU Reviewed; 372 AA. AC Q83BZ9; DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot. DT 01-JUN-2003, sequence version 1. DT 27-MAR-2024, entry version 114. 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=CBU_1338; OS Coxiella burnetii (strain RSA 493 / Nine Mile phase I). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Legionellales; Coxiellaceae; OC Coxiella. OX NCBI_TaxID=227377; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=RSA 493 / Nine Mile phase I; RX PubMed=12704232; DOI=10.1073/pnas.0931379100; RA Seshadri R., Paulsen I.T., Eisen J.A., Read T.D., Nelson K.E., Nelson W.C., RA Ward N.L., Tettelin H., Davidsen T.M., Beanan M.J., DeBoy R.T., RA Daugherty S.C., Brinkac L.M., Madupu R., Dodson R.J., Khouri H.M., RA Lee K.H., Carty H.A., Scanlan D., Heinzen R.A., Thompson H.A., Samuel J.E., RA Fraser C.M., Heidelberg J.F.; RT "Complete genome sequence of the Q-fever pathogen, Coxiella burnetii."; RL Proc. Natl. Acad. Sci. U.S.A. 100:5455-5460(2003). 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 -!- SEQUENCE CAUTION: CC Sequence=AAO90841.2; Type=Erroneous initiation; Evidence={ECO:0000305}; 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; AE016828; AAO90841.2; ALT_INIT; Genomic_DNA. DR RefSeq; NP_820327.2; NC_002971.3. DR PDB; 3TQT; X-ray; 1.88 A; A/B=1-372. DR PDBsum; 3TQT; -. DR AlphaFoldDB; Q83BZ9; -. DR SMR; Q83BZ9; -. DR STRING; 227377.CBU_1338; -. DR EnsemblBacteria; AAO90841; AAO90841; CBU_1338. DR GeneID; 1209244; -. DR KEGG; cbu:CBU_1338; -. DR PATRIC; fig|227377.7.peg.1330; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_0_0_6; -. DR OrthoDB; 9813261at2; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000002671; 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 1: Evidence at protein level; KW 3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation; KW Cytoplasm; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding; KW Peptidoglycan synthesis; Reference proteome. FT CHAIN 1..372 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_0000177813" FT DOMAIN 145..349 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 176..231 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 303 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" 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 316 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 318 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT STRAND 4..12 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 18..31 FT /evidence="ECO:0007829|PDB:3TQT" FT TURN 34..36 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 37..44 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 50..53 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 56..61 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 64..70 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 73..78 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 87..89 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 100..104 FT /evidence="ECO:0007829|PDB:3TQT" FT TURN 109..112 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 115..122 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 127..129 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 132..139 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 141..150 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 159..161 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 170..177 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 183..189 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 193..195 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 196..199 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 202..212 FT /evidence="ECO:0007829|PDB:3TQT" FT TURN 213..215 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 219..223 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 227..239 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 246..249 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 268..271 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 277..293 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 298..306 FT /evidence="ECO:0007829|PDB:3TQT" FT STRAND 312..320 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 328..335 FT /evidence="ECO:0007829|PDB:3TQT" FT HELIX 340..370 FT /evidence="ECO:0007829|PDB:3TQT" SQ SEQUENCE 372 AA; 41218 MW; C983B28F92B519EC CRC64; MAEKLHISVL CGGQSTEHEI SIQSAKNIVN TLDAAKYLIS VIFIDHVGRW YLIDQPEMFL AHSPDHLVKE GSARPITIAF GDAAKPWQSL NGDGRRYSAD CVFPMVHGTQ GEDGALQGLL ELLNLPYVGA NVQSSAVCME KDLTKTVLRA GGIPVVDWHT LSPRDATEGV YQRLLDRWGT SELFVKAVSL GSSVATLPVK TETEFTKAVK EVFRYDDRLM VEPRIRGREI ECAVLGNGAP KASLPGEIIP HHDYYSYDAK YLDPNGATTT TSVDLSESVT KQIQQIAIDA FKMVHCSGMA RVDFFVTPNN KVLVNEINTI PGFTNISMYP KMWEASGLPC PNLLDQLIEL AIDRHQEQQK LIRCYEVKAR SL //