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PDBsum entry 2di3

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protein metals Protein-protein interface(s) links
Transcription PDB id
2di3
Jmol
Contents
Protein chains
231 a.a. *
Metals
_ZN ×2
Waters ×400
* Residue conservation analysis
PDB id:
2di3
Name: Transcription
Title: Crystal structure of the transcriptional factor cgl2915 from corynebacterium glutamicum
Structure: Bacterial regulatory proteins, gntr family. Chain: a, b. Synonym: bacterium transcriptional factor, fadr homologue protein. Engineered: yes
Source: Corynebacterium glutamicum. Organism_taxid: 1718. Strain: atcc 13032. Gene: cgl2915. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.05Å     R-factor:   0.205     R-free:   0.250
Authors: Y.G.Gao,M.Yao,I.Tanaka
Key ref: Y.G.Gao et al. (2008). Structural and functional characterization of the LldR from Corynebacterium glutamicum: a transcriptional repressor involved in L-lactate and sugar utilization. Nucleic Acids Res, 36, 7110-7123. PubMed id: 18988622
Date:
28-Mar-06     Release date:   28-Mar-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8NLM6  (Q8NLM6_CORGL) -  Bacterial regulatory proteins, GntR family
Seq:
Struc:
231 a.a.
231 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     3 terms  

 

 
Nucleic Acids Res 36:7110-7123 (2008)
PubMed id: 18988622  
 
 
Structural and functional characterization of the LldR from Corynebacterium glutamicum: a transcriptional repressor involved in L-lactate and sugar utilization.
Y.G.Gao, H.Suzuki, H.Itou, Y.Zhou, Y.Tanaka, M.Wachi, N.Watanabe, I.Tanaka, M.Yao.
 
  ABSTRACT  
 
LldR (CGL2915) from Corynebacterium glutamicum is a transcription factor belonging to the GntR family, which is typically involved in the regulation of oxidized substrates associated with amino acid metabolism. In the present study, the crystal structure of LldR was determined at 2.05-A resolution. The structure consists of N- and C-domains similar to those of FadR, but with distinct domain orientations. LldR and FadR dimers achieve similar structures by domain swapping, which was first observed in dimeric assembly of transcription factors. A structural feature of Zn(2+) binding in the regulatory domain was also observed, as a difference from the FadR subfamily. DNA microarray and DNase I footprint analyses suggested that LldR acts as a repressor regulating cgl2917-lldD and cgl1934-fruK-ptsF operons, which are indispensable for l-lactate and fructose/sucrose utilization, respectively. Furthermore, the stoichiometries and affinities of LldR and DNAs were determined by isothermal titration calorimetry measurements. The transcriptional start site and repression of LldR on the cgl2917-lldD operon were analysed by primer extension assay. Mutation experiments showed that residues Lys4, Arg32, Arg42 and Gly63 are crucial for DNA binding. The location of the putative ligand binding cavity and the regulatory mechanism of LldR on its affinity for DNA were proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21073308 H.Teramoto, M.Inui, and H.Yukawa (2010).
Regulation of genes involved in sugar uptake, glycolysis and lactate production in Corynebacterium glutamicum.
  Future Microbiol, 5, 1475-1481.  
21159175 O.Kato, J.W.Youn, K.C.Stansen, D.Matsui, T.Oikawa, and V.F.Wendisch (2010).
Quinone-dependent D-lactate dehydrogenase Dld (Cg1027) is essential for growth of Corynebacterium glutamicum on D-lactate.
  BMC Microbiol, 10, 321.  
20213668 R.J.Falconer, A.Penkova, I.Jelesarov, and B.M.Collins (2010).
Survey of the year 2008: applications of isothermal titration calorimetry.
  J Mol Recognit, 23, 395-413.  
19429617 K.Toyoda, H.Teramoto, M.Inui, and H.Yukawa (2009).
The ldhA gene, encoding fermentative L-lactate dehydrogenase of Corynebacterium glutamicum, is under the control of positive feedback regulation mediated by LldR.
  J Bacteriol, 191, 4251-4258.  
19307717 M.Zheng, D.R.Cooper, N.E.Grossoehme, M.Yu, L.W.Hung, M.Cieslik, U.Derewenda, S.A.Lesley, I.A.Wilson, D.P.Giedroc, and Z.S.Derewenda (2009).
Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn(2+)-binding FCD domains.
  Acta Crystallogr D Biol Crystallogr, 65, 356-365.
PDB code: 3fms
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