ID DDL_PARXL Reviewed; 313 AA. AC Q13TZ4; DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot. DT 22-AUG-2006, sequence version 1. DT 27-MAR-2024, entry version 119. 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=Bxeno_A3907; ORFNames=Bxe_A0488; OS Paraburkholderia xenovorans (strain LB400). OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; OC Burkholderiaceae; Paraburkholderia. OX NCBI_TaxID=266265; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=LB400; RX PubMed=17030797; DOI=10.1073/pnas.0606924103; RA Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L., RA Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V., RA Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J., RA Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T., RA Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.; RT "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome RT shaped for versatility."; RL Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(2006). 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; CP000270; ABE32445.1; -; Genomic_DNA. DR RefSeq; WP_011489915.1; NZ_CP008760.1. DR PDB; 4EGJ; X-ray; 2.30 A; A/B/C/D=1-313. DR PDBsum; 4EGJ; -. DR AlphaFoldDB; Q13TZ4; -. DR SMR; Q13TZ4; -. DR STRING; 266265.Bxe_A0488; -. DR KEGG; bxb:DR64_2664; -. DR KEGG; bxe:Bxe_A0488; -. DR PATRIC; fig|266265.5.peg.4128; -. DR eggNOG; COG1181; Bacteria. DR OrthoDB; 9813261at2; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000001817; Chromosome 1. 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:SF23; D-ALANINE--D-ALANINE LIGASE B; 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. FT CHAIN 1..313 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_0000341080" FT DOMAIN 108..308 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 138..193 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 262 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 275 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 275 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 277 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT HELIX 6..9 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 11..15 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 23..39 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 43..47 FT /evidence="ECO:0007829|PDB:4EGJ" FT TURN 49..51 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 56..59 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 64..67 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 72..74 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 78..86 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 89..92 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 95..101 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 104..113 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 121..125 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 130..141 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 143..149 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 164..166 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 167..174 FT /evidence="ECO:0007829|PDB:4EGJ" FT TURN 175..177 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 179..185 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 189..198 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 206..208 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 228..231 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 236..251 FT /evidence="ECO:0007829|PDB:4EGJ" FT TURN 252..254 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 257..266 FT /evidence="ECO:0007829|PDB:4EGJ" FT STRAND 271..279 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 287..294 FT /evidence="ECO:0007829|PDB:4EGJ" FT HELIX 299..308 FT /evidence="ECO:0007829|PDB:4EGJ" SQ SEQUENCE 313 AA; 33535 MW; DDBB5D2E458BD6D3 CRC64; MSSIDPKQFG KVAVLLGGNS AEREVSLNSG RLVLQGLRDA GIDAHPFDPA ERPLAALKEE GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL GLDKFRTKLV WQQLGIPTPP FEAVLRGDDY EARAKEIVAK LGLPLFVKPA SEGSSVAVIK VKSADALPAA LIEAVKFDRI VVVEKSIEGG GEYTACIAGN LDLPVIRIVP AGEFYDYHAK YIANDTQYLI PCGLTADEEA RLKVLARRAF DVLGCTDWGR ADFMLDADGN PYFLEVNTAP GMTDHSLPPK AARAVGISYQ ELVVAVLALT LKD //