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DDL_BURP0
ID   DDL_BURP0               Reviewed;         312 AA.
AC   A3NZL3;
DT   10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT   03-APR-2007, sequence version 1.
DT   03-AUG-2022, entry version 93.
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=BURPS1106A_3548;
OS   Burkholderia pseudomallei (strain 1106a).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Burkholderia; pseudomallei group.
OX   NCBI_TaxID=357348;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=1106a;
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; CP000572; ABN90443.1; -; Genomic_DNA.
DR   RefSeq; WP_004194254.1; NC_009076.1.
DR   PDB; 5NRH; X-ray; 1.30 A; A/B=1-312.
DR   PDB; 5NRI; X-ray; 1.50 A; A/B=1-312.
DR   PDBsum; 5NRH; -.
DR   PDBsum; 5NRI; -.
DR   AlphaFoldDB; A3NZL3; -.
DR   SMR; A3NZL3; -.
DR   EnsemblBacteria; ABN90443; ABN90443; BURPS1106A_3548.
DR   GeneID; 56594282; -.
DR   KEGG; bpl:BURPS1106A_3548; -.
DR   HOGENOM; CLU_039268_1_2_4; -.
DR   OMA; NTTPGMT; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000006738; 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_0000341075"
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:5NRI"
FT   STRAND          11..15
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           23..39
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          43..47
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   TURN            49..51
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           56..59
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          64..67
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           72..74
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           78..85
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          89..92
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           95..101
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           104..113
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          121..125
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           130..141
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          145..151
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          159..161
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           164..166
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           167..177
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          179..185
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          189..198
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          206..209
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          211..215
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           217..221
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          227..231
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           236..252
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          257..266
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   STRAND          271..279
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           287..293
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   TURN            294..296
FT                   /evidence="ECO:0007829|PDB:5NRI"
FT   HELIX           299..308
FT                   /evidence="ECO:0007829|PDB:5NRI"
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
 
 
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