ID DDL_SHEON Reviewed; 336 AA.
AC Q8EEZ2;
DT 15-DEC-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 07-OCT-2020, entry version 107.
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}; Synonyms=ddlA;
GN OrderedLocusNames=SO_2217;
OS Shewanella oneidensis (strain MR-1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=211586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MR-1;
RX PubMed=12368813; DOI=10.1038/nbt749;
RA Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT Shewanella oneidensis.";
RL Nat. Biotechnol. 20:1118-1123(2002).
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}.
DR EMBL; AE014299; AAN55258.1; -; Genomic_DNA.
DR RefSeq; NP_717814.1; NC_004347.2.
DR RefSeq; WP_011072241.1; NC_004347.2.
DR SMR; Q8EEZ2; -.
DR STRING; 211586.SO_2217; -.
DR PaxDb; Q8EEZ2; -.
DR EnsemblBacteria; AAN55258; AAN55258; SO_2217.
DR KEGG; son:SO_2217; -.
DR PATRIC; fig|1028802.3.peg.1771; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_6; -.
DR KO; K01921; -.
DR OMA; IDFFLTD; -.
DR OrthoDB; 764798at2; -.
DR PhylomeDB; Q8EEZ2; -.
DR BioCyc; SONE211586:G1GMP-2030-MONOMER; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000008186; 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; ISS:TIGR.
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; ISS:TIGR.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1490.20; -; 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 Pfam; PF07478; Dala_Dala_lig_C; 1.
DR Pfam; PF01820; Dala_Dala_lig_N; 1.
DR PIRSF; PIRSF039102; Ddl/VanB; 1.
DR SUPFAM; SSF52440; SSF52440; 1.
DR TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 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..336
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000177871"
FT DOMAIN 124..330
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT NP_BIND 154..209
FT /note="ATP"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT METAL 284
FT /note="Magnesium or manganese 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT METAL 297
FT /note="Magnesium or manganese 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT METAL 297
FT /note="Magnesium or manganese 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT METAL 299
FT /note="Magnesium or manganese 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ SEQUENCE 336 AA; 37468 MW; 63CCCDB0A99D2C3D CRC64;
MSKINLLLLC GGGSAEHDIS LLSANYFETS LAKSEQFNVL RVVLDKFGQY QTAAGDDCEL
TNNREIRFRD ESKAPWPVDY VIPCIHGYPG ETGDIQSYFN LIQLPYFGCE SEASSNCFNK
ITAKMWFSAL GIPNTPYIFL NQYDDEAIAQ TQAALEKWGS IFVKAASQGS SVGCYKVDEA
SKVLGVLKDA FGYAPYVIVE KTIKARELEV AVYEYQGEVI ATLPGEIICD SNTFYTFDEK
YAKSSKARTD VVAQNVPTDI SDQIRAYAIK AFKGMKLRHL SRIDFFLTAD NEILLNEINT
FPGSTPISMF PKMLQNHGHD FTQYLSLVIN SQLAAK
//
