DDL_YERPE
ID DDL_YERPE Reviewed; 306 AA.
AC Q8ZIE7; Q0WJB0;
DT 02-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 149.
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=ddlB;
GN OrderedLocusNames=YPO0557, y3624, YP_3627;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
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}.
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DR EMBL; AL590842; CAL19236.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM87172.1; -; Genomic_DNA.
DR EMBL; AE017042; AAS63775.1; -; Genomic_DNA.
DR PIR; AB0069; AB0069.
DR RefSeq; WP_002210432.1; NZ_WUCM01000081.1.
DR RefSeq; YP_002345628.1; NC_003143.1.
DR PDB; 3V4Z; X-ray; 2.69 A; A/B=1-306.
DR PDB; 4ZQI; X-ray; 2.30 A; A/B/C/D=1-306.
DR PDB; 5BPF; X-ray; 2.28 A; A/B/C/D=1-306.
DR PDB; 5BPH; X-ray; 1.70 A; A/B/C/D=1-306.
DR PDB; 5C1O; X-ray; 2.50 A; A/B/C/D=1-306.
DR PDB; 5C1P; X-ray; 2.40 A; A/B/C/D=1-306.
DR PDBsum; 3V4Z; -.
DR PDBsum; 4ZQI; -.
DR PDBsum; 5BPF; -.
DR PDBsum; 5BPH; -.
DR PDBsum; 5C1O; -.
DR PDBsum; 5C1P; -.
DR AlphaFoldDB; Q8ZIE7; -.
DR SMR; Q8ZIE7; -.
DR IntAct; Q8ZIE7; 3.
DR STRING; 214092.YPO0557; -.
DR PaxDb; Q8ZIE7; -.
DR DNASU; 1148571; -.
DR EnsemblBacteria; AAM87172; AAM87172; y3624.
DR EnsemblBacteria; AAS63775; AAS63775; YP_3627.
DR GeneID; 66842889; -.
DR KEGG; ype:YPO0557; -.
DR KEGG; ypk:y3624; -.
DR KEGG; ypm:YP_3627; -.
DR PATRIC; fig|214092.21.peg.810; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_1_2_6; -.
DR OMA; NTTPGMT; -.
DR BRENDA; 6.3.2.4; 4559.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; 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; 3.30.1490.20; -; 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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation;
KW Cytoplasm; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Peptidoglycan synthesis; Reference proteome.
FT CHAIN 1..306
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000177912"
FT DOMAIN 101..303
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 134..189
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 257
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 270
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 270
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 272
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 16..32
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 36..41
FT /evidence="ECO:0007829|PDB:5BPH"
FT TURN 42..44
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:5BPH"
FT TURN 50..54
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:5BPH"
FT TURN 65..67
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 68..70
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 71..79
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 88..93
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 97..106
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 119..124
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 127..134
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 139..147
FT /evidence="ECO:0007829|PDB:5BPH"
FT TURN 150..153
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 163..171
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 175..181
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 187..193
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 212..216
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 222..226
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 231..247
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 252..260
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 266..274
FT /evidence="ECO:0007829|PDB:5BPH"
FT STRAND 278..281
FT /evidence="ECO:0007829|PDB:3V4Z"
FT HELIX 282..290
FT /evidence="ECO:0007829|PDB:5BPH"
FT HELIX 294..303
FT /evidence="ECO:0007829|PDB:5BPH"
SQ SEQUENCE 306 AA; 33150 MW; C78CFF3D2E11F846 CRC64;
MAEKVAVLLG GTSAEREVSL LSGQAVLAGL KEAGIDAYGV DTKDFPVTQL KEQGFDKVFI
ALHGRGGEDG TLQGVLEFLQ LPYTGSGVMA SALTMDKLRT KLVWQALGLP ISPYVALNRQ
QFETLSPEEL VACVAKLGLP LIVKPSHEGS SVGMSKVDHA SELQKALVEA FQHDSDVLIE
KWLSGPEFTV AILGDEVLPS IRIQPPGVFY DYDAKYLSDK TQYFCPSGLS DESEQQLAAL
ALQAYHALDC SGWGRVDVMQ DRDGHFYLLE VNTSPGMTSH SLVPMAARQY GLSFSQLVAR
ILMLAD
