DDL_BURA4
ID DDL_BURA4 Reviewed; 313 AA.
AC B1YSS6;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 20-MAY-2008, sequence version 1.
DT 03-AUG-2022, entry version 84.
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=BamMC406_0490;
OS Burkholderia ambifaria (strain MC40-6).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; Burkholderia cepacia complex.
OX NCBI_TaxID=398577;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MC40-6;
RA Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Lang D., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Ramette A.,
RA Konstantinidis K., Tiedje J., Richardson P.;
RT "Complete sequence of chromosome 1 of Burkholderia ambifaria MC40-6.";
RL Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases.
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP001025; ACB62987.1; -; Genomic_DNA.
DR RefSeq; WP_012363028.1; NC_010551.1.
DR PDB; 4EG0; X-ray; 1.65 A; A/B=1-313.
DR PDBsum; 4EG0; -.
DR AlphaFoldDB; B1YSS6; -.
DR SMR; B1YSS6; -.
DR EnsemblBacteria; ACB62987; ACB62987; BamMC406_0490.
DR KEGG; bac:BamMC406_0490; -.
DR HOGENOM; CLU_039268_1_2_4; -.
DR OMA; NTTPGMT; -.
DR OrthoDB; 764798at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001680; Chromosome 1.
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..313
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_1000091164"
FT DOMAIN 108..308
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 138..193
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 277
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT HELIX 6..9
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 11..15
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 23..39
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:4EG0"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 56..59
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 78..86
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 104..113
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 130..141
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 159..161
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 167..174
FT /evidence="ECO:0007829|PDB:4EG0"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 179..185
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 189..198
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 206..209
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 211..213
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 227..231
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 236..251
FT /evidence="ECO:0007829|PDB:4EG0"
FT TURN 252..254
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 257..265
FT /evidence="ECO:0007829|PDB:4EG0"
FT STRAND 271..279
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 287..294
FT /evidence="ECO:0007829|PDB:4EG0"
FT HELIX 299..308
FT /evidence="ECO:0007829|PDB:4EG0"
SQ SEQUENCE 313 AA; 33393 MW; 494D539CF13A281A CRC64;
MSGIDPKRFG KVAVLFGGES AEREVSLTSG RLVLQGLRDA GIDAHPFDPA ERPLSALKDE
GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL GLDKFRTKLV WQQTGVPTPP
FETVMRGDDY AARATDIVAK LGLPLFVKPA SEGSSVAVLK VKTADALPAA LSEAATHDKI
VIVEKSIEGG GEYTACIAGD LDLPLIKIVP AGEFYDYHAK YVANDTQYLI PCGLPAEQET
ELKRIARRAF DVLGCTDWGR ADFMLDAAGN AYFLEVNTAP GMTDHSLPPK AARSIGIGYS
ELVVKVLSLT LND
