DDL_LEUMM
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 03-AUG-2022, entry version 105.
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=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; Firmicutes; 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 523
RC / 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 STRING; 203120.LEUM_0264; -.
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 OMA; NTTPGMT; -.
DR OrthoDB; 764798at2; -.
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; 3.30.1490.20; -; 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.
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
