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Database: UniProt/SWISS-PROT
Entry: DDL_SHEHH
LinkDB: DDL_SHEHH
Original site: DDL_SHEHH 
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
//
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