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Gene regulation PDB id
2b5a
Jmol
Contents
Protein chains
77 a.a. *
Ligands
ACY ×2
Waters ×229
* Residue conservation analysis
PDB id:
2b5a
Name: Gene regulation
Title: C.Bcli, control element of the bcli restriction-modification
Structure: C.Bcli. Chain: a, b, c, d. Engineered: yes
Source: Bacillus caldolyticus. Organism_taxid: 1394. Gene: bclic. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.54Å     R-factor:   0.167     R-free:   0.201
Authors: M.R.Sawaya,Z.Zhu,F.Mersha,S.H.Chan,R.Dabur,S.Y.Xu,G.K.Balend
Key ref:
M.R.Sawaya et al. (2005). Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site. Structure, 13, 1837-1847. PubMed id: 16338412 DOI: 10.1016/j.str.2005.08.017
Date:
28-Sep-05     Release date:   03-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     DNA binding     2 terms  

 

 
DOI no: 10.1016/j.str.2005.08.017 Structure 13:1837-1847 (2005)
PubMed id: 16338412  
 
 
Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site.
M.R.Sawaya, Z.Zhu, F.Mersha, S.H.Chan, R.Dabur, S.Y.Xu, G.K.Balendiran.
 
  ABSTRACT  
 
Protection from DNA invasion is afforded by restriction-modification systems in many bacteria. The efficiency of protection depends crucially on the relative expression levels of restriction versus methytransferase genes. This regulation is provided by a controller protein, named C protein. Studies of the Bcll system in E. coli suggest that C.Bcll functions as a negative regulator for M.Bcll expression, implying that it plays a role in defense against foreign DNA during virus infection. C.Bcll binds (Kd = 14.3 nM) to a 2-fold symmetric C box DNA sequence that overlaps with the putative -35 promoter region upstream of the bcllM and bcllC genes. The C.Bcll fold comprises five alpha helices: two helices form a helix-turn-helix motif, and the remaining three helices form the extensive dimer interface. The C.Bcll-DNA model proposed suggests that DNA bending might play an important role in gene regulation, and that Glu27 and Asp31 in C.Bcll might function critically in the regulation.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Structure of C Protein
(A) Ribbon diagram of the C.BclI dimer, viewed from two orthogonal perspectives. Secondary structural elements are labeled for molecule A. The HTH motif is formed by helix B (red), loop 2 (green), and helix C (recognition helix, blue). The remaining three helices (yellow) form the dimer interface. The 2-fold symmetry axis is indicated by the black ellipse and the vertical line.
(B) Superposition of C.BclI (yellow) and C.Ahd1 (1y7y, orange), the HTH3 family transcription factor (1y9q, green), the SinR transcription regulator (1b0n, blue), cylr2 (1utx, red), and the l repressor (1lmb, purple).
(C) Sequence alignment of C.BclI with other C proteins and structure-based sequence alignment with proteins shown in (B) (bottom). Residues involved in dimer contacts are colored green in the C.BclI sequence.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1837-1847) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21059708 K.Ishikawa, E.Fukuda, and I.Kobayashi (2010).
Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems.
  DNA Res, 17, 325-342.  
21092102 M.K.Kaw, and R.M.Blumenthal (2010).
Translational independence between overlapping genes for a restriction endonuclease and its transcriptional regulator.
  BMC Mol Biol, 11, 87.  
19747545 P.Zhang, P.H.Too, J.C.Samuelson, S.H.Chan, T.Vincze, S.Doucette, S.Bäckström, K.D.Potamousis, T.M.Schramm, D.Forrest, D.C.Schwartz, and S.Y.Xu (2010).
Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.
  Protein Expr Purif, 69, 226-234.  
20497557 Z.Zhu, C.S.Pedamallu, A.Fomenkov, J.Benner, and S.Y.Xu (2010).
Cloning of NruI and Sbo13I restriction and modification sstems in E. coli and amino acid sequence comparison of M.NruI and M.Sbo13I with other amino-methyltransferases.
  BMC Res Notes, 3, 139.  
19336410 E.Bogdanova, M.Zakharova, S.Streeter, J.Taylor, T.Heyduk, G.Kneale, and K.Severinov (2009).
Transcription regulation of restriction-modification system Esp1396I.
  Nucleic Acids Res, 37, 3354-3366.  
19126580 I.Mruk, and R.M.Blumenthal (2009).
Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system.
  Nucleic Acids Res, 37, 983-998.  
19690367 N.Ball, S.D.Streeter, G.G.Kneale, and J.E.McGeehan (2009).
Structure of the restriction-modification controller protein C.Esp1396I.
  Acta Crystallogr D Biol Crystallogr, 65, 900-905.  
  19724127 S.D.Streeter, J.E.McGeehan, and G.G.Kneale (2009).
Overexpression, purification and preliminary X-ray diffraction analysis of the controller protein C.Csp231I from Citrobacter sp. RFL231.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 898-901.  
19019826 S.Russo, J.E.Schweitzer, T.Polen, M.Bott, and E.Pohl (2009).
Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes.
  J Biol Chem, 284, 5208-5216.
PDB codes: 3f51 3f52
19056824 V.Sorokin, K.Severinov, and M.S.Gelfand (2009).
Systematic prediction of control proteins and their DNA binding sites.
  Nucleic Acids Res, 37, 441-451.  
18334533 I.Mruk, and R.M.Blumenthal (2008).
Real-time kinetics of restriction-modification gene expression after entry into a new host cell.
  Nucleic Acids Res, 36, 2581-2593.  
18644840 J.E.McGeehan, S.D.Streeter, S.J.Thresh, N.Ball, R.B.Ravelli, and G.G.Kneale (2008).
Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
  Nucleic Acids Res, 36, 4778-4787.
PDB code: 3clc
17933763 I.Mruk, P.Rajesh, and R.M.Blumenthal (2007).
Regulatory circuit based on autogenous activation-repression: roles of C-boxes and spacer sequences in control of the PvuII restriction-modification system.
  Nucleic Acids Res, 35, 6935-6952.  
17468281 I.Mruk, and T.Kaczorowski (2007).
A rapid and efficient method for cloning genes of type II restriction-modification systems by use of a killer plasmid.
  Appl Environ Microbiol, 73, 4286-4293.  
17855396 S.H.Chan, Y.Bao, E.Ciszak, S.Laget, and S.Y.Xu (2007).
Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.
  Nucleic Acids Res, 35, 6238-6248.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.