ID DDL_SHEHH Reviewed; 333 AA.
AC B0TRK1;
DT 20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT 08-APR-2008, sequence version 1.
DT 18-JUN-2025, 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}; OrderedLocusNames=Shal_1854;
OS Shewanella halifaxensis (strain HAW-EB4).
OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC Alteromonadales; Shewanellaceae; Shewanella.
OX NCBI_TaxID=458817;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HAW-EB4;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C.,
RA Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Kim E., Zhao J.-S., Richardson P.;
RT "Complete sequence of Shewanella halifaxensis HAW-EB4.";
RL Submitted (JAN-2008) to the EMBL/GenBank/DDBJ databases.
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}.
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DR EMBL; CP000931; ABZ76419.1; -; Genomic_DNA.
DR RefSeq; WP_012276951.1; NC_010334.1.
DR AlphaFoldDB; B0TRK1; -.
DR SMR; B0TRK1; -.
DR STRING; 458817.Shal_1854; -.
DR KEGG; shl:Shal_1854; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_6; -.
DR OrthoDB; 9813261at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001317; Chromosome.
DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
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 NCBIfam; NF002527; PRK01966.1-3; 1.
DR NCBIfam; NF002528; PRK01966.1-4; 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; Cell shape; Cell wall biogenesis/degradation; Cytoplasm;
KW Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Peptidoglycan synthesis.
FT CHAIN 1..333
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_1000074788"
FT DOMAIN 124..329
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 154..209
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 283
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 298
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ SEQUENCE 333 AA; 37583 MW; 8897FB4F2AC845B8 CRC64;
MTQKNLLLLC GGGGDEHSIS LLSANFFETQ LATLPHFNVL RVELNAKGQY RTQAGELCEL
TNSKQIRFND QSKAPWDVDY VIPCIHGYPG ETGDIQSYFE LINLPYFGCD SEASSNCFNK
VTAKMWFSAL GIRNTPYIFL NEFNQQAIEE TERALEKWGS IFIKAASQGS SVGCYRVDNK
EQLANSLEEA FKYSPYVVVE KTINARELEV AAYEVDGEII ATKPGEIICA SNTFYSFDEK
YAENSQAQTV IEADVDEVIA KQIQEYAIKA FKGMKLRHLS RIDFFLTDEN EILLNEINTF
PGQTQISMFP KMLQNHGHNF AQYLSGNIMA QLK
//
