ID DDL_PORG3 Reviewed; 330 AA. AC B2RIT4; DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot. DT 01-JUL-2008, sequence version 1. DT 02-SEP-2026, entry version 90. 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=PGN_0760; OS Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM OS 12257 / NCTC 11834 / 2561). OC Bacteria; Pseudomonadati; Bacteroidota; Bacteroidia; Bacteroidales; OC Porphyromonadaceae; Porphyromonas. OX NCBI_TaxID=431947; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / RC 2561; RX PubMed=18524787; DOI=10.1093/dnares/dsn013; RA Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., RA Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., RA Nakayama K.; RT "Determination of the genome sequence of Porphyromonas gingivalis strain RT ATCC 33277 and genomic comparison with strain W83 revealed extensive genome RT rearrangements in P. gingivalis."; RL DNA Res. 15:215-225(2008). CC -!- FUNCTION: Cell wall formation. {ECO:0000255|HAMAP-Rule:MF_00047}. CC -!- CATALYTIC ACTIVITY: CC Reaction=2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate + CC H(+); Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57416, ChEBI:CHEBI:57822, CC ChEBI:CHEBI:456216; EC=6.3.2.4; Evidence={ECO:0000255|HAMAP- CC 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; AP009380; BAG33279.1; -; Genomic_DNA. DR RefSeq; WP_012457758.1; NC_010729.1. DR AlphaFoldDB; B2RIT4; -. DR SMR; B2RIT4; -. DR GeneID; 29255979; -. DR KEGG; pgn:PGN_0760; -. DR eggNOG; COG1181; Bacteria. DR HOGENOM; CLU_039268_1_1_10; -. DR OrthoDB; 9813261at2; -. DR BioCyc; PGIN431947:G1G2V-833-MONOMER; -. DR UniPathway; UPA00219; -. DR Proteomes; UP000008842; Chromosome. DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell. DR GO; GO:0005524; F:ATP binding; IEA:InterPro. DR GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule. DR GO; GO:0046872; F:metal ion binding; IEA:InterPro. DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule. 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; NF002527; PRK01966.1-3; 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 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..330 FT /note="D-alanine--D-alanine ligase" FT /id="PRO_1000091202" FT DOMAIN 122..323 FT /note="ATP-grasp" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 151..206 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 277 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 290 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 290 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" FT BINDING 292 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047" SQ SEQUENCE 330 AA; 36369 MW; 36097B6499FDB9EE CRC64; MKKPIVAVIA GGYSGEHSVS LKSAAGILSW LGSEPFSAFL VLIERDRWSV RVSEQREVPL DKNDFSFDLD DERIRFDYAY ITIHGTPGEN GLLQGYLDMI GIPYNTGDTL VESLTFNKYV CNRFLSGFGI RIADSMRLTG RDTQPDVADL TARMGLPLFV KPNVGGSSIA TTKVVEAAQL LPAIGQAFSE GEEVMIERLI CGTEVTCGAF LRKKEVVALP VTEVVAHNEF FDFDAKYNGA VEEITPARIS DEATRLIQTM TARIYELLNA RGIIRVDYII EADGIPTLLE VNTTPGMTPT SFIPQQVRAA EMDMKEVLCT IIRDGLNETQ //