ID DDLB_SALTY Reviewed; 306 AA.
AC Q8ZRU1;
DT 02-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 27-MAR-2024, entry version 133.
DE RecName: Full=D-alanine--D-alanine ligase B;
DE EC=6.3.2.4;
DE AltName: Full=D-Ala-D-Ala ligase B;
DE AltName: Full=D-alanylalanine synthetase B;
GN Name=ddlB; OrderedLocusNames=STM0130;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
CC -!- FUNCTION: Cell wall formation. {ECO:0000250}.
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 -!- 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 -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC {ECO:0000305}.
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DR EMBL; AE006468; AAL19094.1; -; Genomic_DNA.
DR RefSeq; NP_459135.1; NC_003197.2.
DR RefSeq; WP_000763905.1; NC_003197.2.
DR AlphaFoldDB; Q8ZRU1; -.
DR SMR; Q8ZRU1; -.
DR STRING; 99287.STM0130; -.
DR PaxDb; 99287-STM0130; -.
DR GeneID; 1251648; -.
DR KEGG; stm:STM0130; -.
DR PATRIC; fig|99287.12.peg.136; -.
DR HOGENOM; CLU_039268_1_2_6; -.
DR OMA; RVDFFYV; -.
DR PhylomeDB; Q8ZRU1; -.
DR BioCyc; SENT99287:STM0130-MONOMER; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001014; 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; IBA:GO_Central.
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; IBA:GO_Central.
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 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 INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..306
FT /note="D-alanine--D-alanine ligase B"
FT /id="PRO_0000177870"
FT DOMAIN 101..303
FT /note="ATP-grasp"
FT BINDING 134..189
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 257
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 270
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 270
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 272
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
SQ SEQUENCE 306 AA; 32635 MW; AE590226C6D957B6 CRC64;
MADKIAVLLG GTSAERDVSL NSGAAVLAGL REGGINAHPV DPQEVDVAQL KAMGFQKVFI
ALHGRGGEDG TLQGMLELLG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA
EFEKGLSEEQ KARISALGLP LIVKPSREGS SVGMTKVVEE NALQGALSLA FQHDDEILIE
KWLCGPEFTV AIVGEEILPS IRIQPAGTFY DYEAKYLSDE TQYFCPAGLD ASQEAALQSL
VLQAWKALGC TGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR
ILELAD
//
