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   27-MAR-2024, entry version 156.
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; Pseudomonadota; 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; 214092-YPO0557; -.
DR   DNASU; 1148571; -.
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; RVDFFYV; -.
DR   OrthoDB; 9813261at2; -.
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; 3.40.50.20; -; 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; 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
//