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DDL_LEPBA
ID   DDL_LEPBA               Reviewed;         349 AA.
AC   B0S9U5;
DT   10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT   08-APR-2008, sequence version 1.
DT   03-AUG-2022, entry version 80.
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}; OrderedLocusNames=LBF_1808;
OS   Leptospira biflexa serovar Patoc (strain Patoc 1 / Ames).
OC   Bacteria; Spirochaetes; Leptospirales; Leptospiraceae; Leptospira.
OX   NCBI_TaxID=355278;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Patoc 1 / Ames;
RX   PubMed=18270594; DOI=10.1371/journal.pone.0001607;
RA   Picardeau M., Bulach D.M., Bouchier C., Zuerner R.L., Zidane N.,
RA   Wilson P.J., Creno S., Kuczek E.S., Bommezzadri S., Davis J.C., McGrath A.,
RA   Johnson M.J., Boursaux-Eude C., Seemann T., Rouy Z., Coppel R.L.,
RA   Rood J.I., Lajus A., Davies J.K., Medigue C., Adler B.;
RT   "Genome sequence of the saprophyte Leptospira biflexa provides insights
RT   into the evolution of Leptospira and the pathogenesis of leptospirosis.";
RL   PLoS ONE 3:E1607-E1607(2008).
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; CP000777; ABZ94315.1; -; Genomic_DNA.
DR   RefSeq; WP_012388845.1; NC_010842.1.
DR   AlphaFoldDB; B0S9U5; -.
DR   SMR; B0S9U5; -.
DR   KEGG; lbf:LBF_1808; -.
DR   HOGENOM; CLU_039268_1_1_12; -.
DR   OMA; NTTPGMT; -.
DR   BioCyc; LBIF355278:LBF_RS09205-MON; -.
DR   UniPathway; UPA00219; -.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule.
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; IEA:UniProtKB-UniRule.
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.
FT   CHAIN           1..349
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_0000341126"
FT   DOMAIN          140..345
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         169..224
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         300
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         312
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         312
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         314
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ   SEQUENCE   349 AA;  38026 MW;  62516629678BF0D9 CRC64;
     MSKIKIALLF GGISGEHIIS VRSSAFIFAT IDREKYDVCP VYINPNGKFW IPTVSEPIYP
     DPSGKTEIEF LQEFNKANAI VSPSEPADIS QMGFLSAFLG LHGGAGEDGR IQGFLDTLGI
     PHTGSGVLAS SLAMDKYRAN ILFEAMGIPV APFLELEKGK TDPRKTLLNL SFSYPVFIKP
     TLGGSSVNTG MAKTAEEAMT LVDKIFVTDD RVLVQKLVSG TEVSIGVLEK PEGKKRNPFP
     LVPTEIRPKS EFFDFEAKYT KGASEEITPA PVGDEVTKTL QEYTLRCHEI LGCKGYSRTD
     FIISDGVPYV LETNTLPGMT GTSLIPQQAK ALGINMKDVF TWLLEISLS
 
 
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