ID   DDL_LEUMM               Reviewed;         377 AA.
AC   Q03ZI1;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   14-NOV-2006, sequence version 1.
DT   27-MAR-2024, entry version 112.
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};
GN   OrderedLocusNames=LEUM_0264;
OS   Leuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / DSM
OS   20343 / BCRC 11652 / CCM 1803 / JCM 6124 / NCDO 523 / NBRC 100496 / NCIMB
OS   8023 / NCTC 12954 / NRRL B-1118 / 37Y).
OC   Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae;
OC   Leuconostoc.
OX   NCBI_TaxID=203120;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 8293 / DSM 20343 / BCRC 11652 / CCM 1803 / JCM 6124 / NCDO
RC   523 / NBRC 100496 / NCIMB 8023 / NCTC 12954 / NRRL B-1118 / 37Y;
RX   PubMed=17030793; DOI=10.1073/pnas.0607117103;
RA   Makarova K.S., Slesarev A., Wolf Y.I., Sorokin A., Mirkin B., Koonin E.V.,
RA   Pavlov A., Pavlova N., Karamychev V., Polouchine N., Shakhova V.,
RA   Grigoriev I., Lou Y., Rohksar D., Lucas S., Huang K., Goodstein D.M.,
RA   Hawkins T., Plengvidhya V., Welker D., Hughes J., Goh Y., Benson A.,
RA   Baldwin K., Lee J.-H., Diaz-Muniz I., Dosti B., Smeianov V., Wechter W.,
RA   Barabote R., Lorca G., Altermann E., Barrangou R., Ganesan B., Xie Y.,
RA   Rawsthorne H., Tamir D., Parker C., Breidt F., Broadbent J.R., Hutkins R.,
RA   O'Sullivan D., Steele J., Unlu G., Saier M.H. Jr., Klaenhammer T.,
RA   Richardson P., Kozyavkin S., Weimer B.C., Mills D.A.;
RT   "Comparative genomics of the lactic acid bacteria.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:15611-15616(2006).
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; CP000414; ABJ61391.1; -; Genomic_DNA.
DR   RefSeq; WP_011679162.1; NC_008531.1.
DR   PDB; 1EHI; X-ray; 2.38 A; A/B=1-377.
DR   PDBsum; 1EHI; -.
DR   AlphaFoldDB; Q03ZI1; -.
DR   SMR; Q03ZI1; -.
DR   EnsemblBacteria; ABJ61391; ABJ61391; LEUM_0264.
DR   GeneID; 61177257; -.
DR   KEGG; lme:LEUM_0264; -.
DR   eggNOG; COG1181; Bacteria.
DR   HOGENOM; CLU_039268_0_1_9; -.
DR   UniPathway; UPA00219; -.
DR   EvolutionaryTrace; Q03ZI1; -.
DR   Proteomes; UP000000362; Chromosome.
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; 3.40.50.20; -; 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:SF25; D-ALANINE--D-ALANINE LIGASE A; 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.
FT   CHAIN           1..377
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_1000030463"
FT   DOMAIN          140..349
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         170..225
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         303
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         316
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         316
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         318
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..11
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           17..34
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          35..44
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           53..60
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           65..73
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           86..89
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          95..100
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   TURN            104..106
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          107..109
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           110..117
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          122..124
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           127..134
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           136..144
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   TURN            145..147
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          153..156
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           160..163
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           166..173
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          177..183
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   TURN            186..189
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          190..193
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           196..206
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   TURN            207..209
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          213..217
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          224..234
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          236..244
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          248..252
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           257..260
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          268..272
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           277..293
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          298..306
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   STRAND          312..320
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           328..330
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           332..336
FT                   /evidence="ECO:0007829|PDB:1EHI"
FT   HELIX           340..360
FT                   /evidence="ECO:0007829|PDB:1EHI"
SQ   SEQUENCE   377 AA;  41826 MW;  D1C6A40A6812AE01 CRC64;
     MTKKRVALIF GGNSSEHDVS KRSAQNFYNA IEATGKYEII VFAIAQNGFF LDTESSKKIL
     ALEDEQPIVD AFMKTVDASD PLARIHALKS AGDFDIFFPV VHGNLGEDGT LQGLFKLLDK
     PYVGAPLRGH AVSFDKALTK ELLTVNGIRN TKYIVVDPES ANNWSWDKIV AELGNIVFVK
     AANQGSSVGI SRVTNAEEYT EALSDSFQYD YKVLIEEAVN GARELEVGVI GNDQPLVSEI
     GAHTVPNQGS GDGWYDYNNK FVDNSAVHFE IPAQLSPEVT KEVKQMALDA YKVLNLRGEA
     RMDFLLDENN VPYLGEPNTL PGFTNMSLFK RLWDYSDINN AKLVDMLIDY GFEDFAQNKK
     LSYSFVSLGE EKIGKFN
//