ID DDLB_ECOLI Reviewed; 306 AA.
AC P07862;
DT 01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 27-MAR-2024, entry version 200.
DE RecName: Full=D-alanine--D-alanine ligase B;
DE EC=6.3.2.4 {ECO:0000269|PubMed:1554356};
DE AltName: Full=D-Ala-D-Ala ligase B;
DE AltName: Full=D-alanylalanine synthetase B;
GN Name=ddlB; Synonyms=ddl; OrderedLocusNames=b0092, JW0090;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3528126; DOI=10.1128/jb.167.3.809-817.1986;
RA Robinson A.C., Kenan D.J., Sweeney J., Donachie W.D.;
RT "Further evidence for overlapping transcriptional units in an Escherichia
RT coli cell envelope-cell division gene cluster: DNA sequence and
RT transcriptional organization of the ddl ftsQ region.";
RL J. Bacteriol. 167:809-817(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1630901; DOI=10.1093/nar/20.13.3305;
RA Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K.,
RA Mizobuchi K., Nakata A.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 0-
RT 2.4 min region.";
RL Nucleic Acids Res. 20:3305-3308(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-41.
RC STRAIN=K12;
RX PubMed=2197603; DOI=10.1093/nar/18.13.4014;
RA Ikeda M., Wachi M., Jung H.K., Ishino F., Matsuhashi M.;
RT "Nucleotide sequence involving murG and murC in the mra gene cluster region
RT of Escherichia coli.";
RL Nucleic Acids Res. 18:4014-4014(1990).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 300-306.
RX PubMed=2228979; DOI=10.1128/jb.172.11.6611-6614.1990;
RA Dewar S.J., Donachie W.D.;
RT "Regulation of expression of the ftsA cell division gene by sequences in
RT upstream genes.";
RL J. Bacteriol. 172:6611-6614(1990).
RN [7]
RP CHARACTERIZATION, PARTIAL PROTEIN SEQUENCE, AND CATALYTIC ACTIVITY.
RX PubMed=1554356; DOI=10.1042/bj2820747;
RA Al-Bar O.A., O'Connor C.D., Giles I.G., Akhtar M.;
RT "D-alanine:D-alanine ligase of Escherichia coli. Expression, purification
RT and inhibitory studies on the cloned enzyme.";
RL Biochem. J. 282:747-752(1992).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
RX PubMed=7939684; DOI=10.1126/science.7939684;
RA Fan C., Moews P.C., Walsh C.T., Knox J.R.;
RT "Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3-A
RT resolution.";
RL Science 266:439-443(1994).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=9054558; DOI=10.1021/bi962431t;
RA Fan C., Park I.-S., Walsh C.T., Knox J.R.;
RT "D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with
RT wild type and the Y216F mutant.";
RL Biochemistry 36:2531-2538(1997).
CC -!- FUNCTION: Cell wall formation.
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:0000269|PubMed:1554356};
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.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC {ECO:0000305}.
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DR EMBL; M14029; AAA23672.1; -; Genomic_DNA.
DR EMBL; K02668; AAA23815.1; -; Genomic_DNA.
DR EMBL; X52644; CAA36869.1; -; Genomic_DNA.
DR EMBL; X55034; CAA38869.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73203.1; -; Genomic_DNA.
DR EMBL; AP009048; BAB96660.1; -; Genomic_DNA.
DR PIR; A30289; CEECDL.
DR RefSeq; NP_414634.1; NC_000913.3.
DR RefSeq; WP_000130056.1; NZ_STEB01000010.1.
DR PDB; 1IOV; X-ray; 2.20 A; A=1-306.
DR PDB; 1IOW; X-ray; 1.90 A; A=1-306.
DR PDB; 2DLN; X-ray; 2.30 A; A=1-306.
DR PDB; 4C5A; X-ray; 1.65 A; A/B=1-306.
DR PDB; 4C5B; X-ray; 1.50 A; A/B=1-306.
DR PDB; 4C5C; X-ray; 1.40 A; A/B=1-306.
DR PDBsum; 1IOV; -.
DR PDBsum; 1IOW; -.
DR PDBsum; 2DLN; -.
DR PDBsum; 4C5A; -.
DR PDBsum; 4C5B; -.
DR PDBsum; 4C5C; -.
DR AlphaFoldDB; P07862; -.
DR SMR; P07862; -.
DR BioGRID; 4261114; 306.
DR BioGRID; 850681; 3.
DR IntAct; P07862; 4.
DR STRING; 511145.b0092; -.
DR BindingDB; P07862; -.
DR ChEMBL; CHEMBL1956; -.
DR DrugCentral; P07862; -.
DR jPOST; P07862; -.
DR PaxDb; 511145-b0092; -.
DR EnsemblBacteria; AAC73203; AAC73203; b0092.
DR GeneID; 75202091; -.
DR GeneID; 946324; -.
DR KEGG; ecj:JW0090; -.
DR KEGG; eco:b0092; -.
DR PATRIC; fig|1411691.4.peg.2188; -.
DR EchoBASE; EB0210; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_1_2_6; -.
DR InParanoid; P07862; -.
DR OMA; RVDFFYV; -.
DR OrthoDB; 9813261at2; -.
DR PhylomeDB; P07862; -.
DR BioCyc; EcoCyc:DALADALALIGB-MONOMER; -.
DR BioCyc; MetaCyc:DALADALALIGB-MONOMER; -.
DR BRENDA; 6.3.2.4; 2026.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; P07862; -.
DR PRO; PR:P07862; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IMP:EcoCyc.
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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation;
KW Cytoplasm; Direct protein sequencing; Ligase; Magnesium; Manganese;
KW Metal-binding; Nucleotide-binding; Peptidoglycan synthesis;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..306
FT /note="D-alanine--D-alanine ligase B"
FT /id="PRO_0000177818"
FT DOMAIN 101..303
FT /note="ATP-grasp"
FT ACT_SITE 15
FT ACT_SITE 150
FT ACT_SITE 281
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"
FT STRAND 4..8
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 16..32
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:4C5C"
FT TURN 42..44
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:4C5C"
FT TURN 50..54
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:4C5C"
FT TURN 65..67
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 71..79
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 97..106
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 119..124
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 128..136
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 139..147
FT /evidence="ECO:0007829|PDB:4C5C"
FT TURN 150..153
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 163..171
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 175..181
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 187..193
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 212..216
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 222..226
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 231..248
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 252..260
FT /evidence="ECO:0007829|PDB:4C5C"
FT STRAND 266..274
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 282..289
FT /evidence="ECO:0007829|PDB:4C5C"
FT HELIX 294..303
FT /evidence="ECO:0007829|PDB:4C5C"
SQ SEQUENCE 306 AA; 32840 MW; F2D401C323A04471 CRC64;
MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI
ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA
EFEKGLSDKQ LAEISALGLP VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE
KWLSGPEFTV AILGEEILPS IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL
VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR
ILELAD
//
