DDL_BURP1
ID DDL_BURP1 Reviewed; 312 AA.
AC Q3JNE1;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 104.
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=BURPS1710b_3542;
OS Burkholderia pseudomallei (strain 1710b).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; pseudomallei group.
OX NCBI_TaxID=320372;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1710b;
RX PubMed=20333227; DOI=10.1093/gbe/evq003;
RA Losada L., Ronning C.M., DeShazer D., Woods D., Fedorova N., Kim H.S.,
RA Shabalina S.A., Pearson T.R., Brinkac L., Tan P., Nandi T., Crabtree J.,
RA Badger J., Beckstrom-Sternberg S., Saqib M., Schutzer S.E., Keim P.,
RA Nierman W.C.;
RT "Continuing evolution of Burkholderia mallei through genome reduction and
RT large-scale rearrangements.";
RL Genome Biol. Evol. 2:102-116(2010).
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; CP000124; ABA49167.1; -; Genomic_DNA.
DR RefSeq; WP_004194254.1; NC_007434.1.
DR PDB; 4EGQ; X-ray; 2.20 A; A/B/C/D=1-312.
DR PDBsum; 4EGQ; -.
DR AlphaFoldDB; Q3JNE1; -.
DR SMR; Q3JNE1; -.
DR EnsemblBacteria; ABA49167; ABA49167; BURPS1710b_3542.
DR GeneID; 56594282; -.
DR KEGG; bpm:BURPS1710b_3542; -.
DR HOGENOM; CLU_039268_1_2_4; -.
DR OMA; NTTPGMT; -.
DR OrthoDB; 764798at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000002700; Chromosome I.
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..312
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000341076"
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 STRAND 11..15
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 23..39
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:4EGQ"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 56..59
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 78..85
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 104..114
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 130..141
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 143..149
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 159..161
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 167..177
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 179..185
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 192..198
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 236..252
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 257..265
FT /evidence="ECO:0007829|PDB:4EGQ"
FT STRAND 271..279
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 287..294
FT /evidence="ECO:0007829|PDB:4EGQ"
FT HELIX 299..308
FT /evidence="ECO:0007829|PDB:4EGQ"
SQ SEQUENCE 312 AA; 33341 MW; CCD89397BEAE5E22 CRC64;
MSGIDPKRFG KVAVLLGGDS AEREVSLNSG RLVLQGLRDA GIDAHPFDPA QRPLAALKDE
GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL GLDKFRTKLV WQQTGIPTPP
FETVMRGDDY AARAQDIVAK LGVPLFVKPA SEGSSVAVEK VKSADALPAA LEEAAKHDKI
VIVEKSIEGG GEYTACIAAD LDLPLIRIVP AGEFYDYHAK YIANDTQYLI PCGLDAAKEA
EFKRIARRAF DVLGCTDWGR ADFMLDAAGN PYFLEVNTAP GMTDHSLPPK AARAVGIGYS
ELVVKVLSLT LD
