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Title: Structures of carbon catabolite protein A–(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gkq1177· OSTI ID:1625474
 [1];  [1];  [2];  [3];  [1]
  1. Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center. Dept. of Biochemistry and Molecular Biology
  2. Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen (Germany). Institut fur Biologie. Lehrstuhl fur Mikrobiologie
  3. Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen (Germany). Institut fur Biologie. Lehrstuhl fur Mikrobiologie
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In Gram-positive bacteria, carbon catabolite protein A (CcpA) is the master regulator of carbon catabolite control, which ensures optimal energy usage under diverse conditions. Unlike other LacI-GalR proteins, CcpA is activated for DNA binding by first forming a complex with the phosphoprotein HPr-Ser46-P. Bacillus subtilis CcpA functions as both a transcription repressor and activator and binds to more than 50 operators called catabolite response elements (cres). These sites are highly degenerate with the consensus, WTGNNARCGNWW WCAW. How CcpA–(HPr-Ser46-P) binds such diverse sequences is unclear. To gain insight into this question, we solved the structures of the CcpA–(HPr-Ser46-P) complex bound to three different operators, the synthetic (syn) cre, ackA2 cre and gntR-down cre. Strikingly, the structures show that the CcpA-bound operators display different bend angles, ranging from 31 to 56. These differences are accommodated by a flexible linkage between the CcpA helix-turn-helix-loop-helix motif and hinge helices, which allows independent docking of these DNA-binding modules. This flexibility coupled with an abundance of non-polar residues capable of non-specific nucleobase interactions permits CcpA–(HPr-Ser46-P) to bind diverse operators. Indeed, biochemical data show that CcpA–(HPr-Ser46-P) binds the three cre sites with similar affinities. Thus, the data reveal properties that license this protein to function as a global transcription regulator.

Research Organization:
Univ. of Texas, Houston, TX (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625474
Journal Information:
Nucleic Acids Research, Vol. 39, Issue 7; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

References (58)

Crystallographic analysis of Lac repressor bound to natural operator O111Edited by J. Doudna journal October 2001
Structure of the sporulation-specific transcription factor Ndt80 bound to DNA journal November 2002
Phosphorylation of either Crh or HPr mediates binding of CcpA to the Bacillus subtilis xyn cre and catabolite repression of the xyn operon 1 1Edited by I. B. Holland journal February 1999
Regulation of Carbon Catabolism in Bacillus Species journal October 2000
The mechanisms of carbon catabolite repression in bacteria journal April 2008
Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses: Catabolite repression mediated by CcpA protein in B. subtilis journal March 2001
Structural Basis for Allosteric Control of the Transcription Regulator CcpA by the Phosphoprotein HPr-Ser46-P journal September 2004
Coupling Physiology and Gene Regulation in Bacteria: The Phosphotransferase Sugar Uptake System Delivers the Signals journal December 1998
Quantitative interdependence of coeffectors, CcpA and cre in carbon catabolite regulation of Bacillus subtilis: Regulatory differences of HPrSerP and CrhP journal April 2005
Organization and transcription of the myo-inositol operon, iol, of Bacillus subtilis. journal July 1997
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination journal September 1998
Conformational analysis of nucleic acids revisited: Curves+ journal July 2009
Improved methods for building protein models in electron density maps and the location of errors in these models journal March 1991
Structural analysis of B. subtilis CcpA effector binding site journal June 2006
The phosphotransferase system (PTS) of Streptomyces coelicolor . Identification and biochemical analysis of a histidine phosphocarrier protein HPr encoded by the gene ptsH journal October 1999
Regulation of the putative bglPH operon for aryl-beta-glucoside utilization in Bacillus subtilis. journal January 1995
Protein kinase-dependent HPr/CcpA interaction links glycolytic activity to carbon catabolite repression in Gram-positive bacteria journal March 1995
Mechanism of corepressor-mediated specific DNA binding by the purine repressor journal October 1995
Charting a course through RNA polymerase journal September 2000
Binding of the Catabolite Repressor Protein CcpA to Its DNA Target Is Regulated by Phosphorylation of its Corepressor HPr journal October 1997
Two different mechanisms mediate catabolite repression of the Bacillus subtilis levanase operon. journal January 1995
A novel protein kinase that controls carbon catabolite repression in bacteria journal March 1998
Evidence that Bacillus catabolite control protein CcpA interacts with RNA polymerase to inhibit transcription: Transcription inhibition by CcpA in vitro journal February 2005
Regulation of the Bacillus subtilis acetate kinase gene by CcpA. journal January 1993
Recognition of 5′-YpG-3′ Sequences by Coupled Stacking/Hydrogen Bonding Interactions with Amino Acid Residues journal January 2004
Catabolite activator protein: DNA binding and transcription activation journal February 2004
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes journal September 1998
Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices journal November 1994
Catabolite repression of the Bacillus subtilis gnt operon exerted by two catabolite-responsive elements journal March 1997
Carbon Catabolite Control of the Metabolic Network in Bacillus subtilis journal February 2009
Catabolite repression-resistant mutations of the Bacillus subtilis alpha-amylase promoter affect transcription levels and are in an operator-like sequence journal December 1987
Systematic study of gene expression and transcription organization in the gntZ–ywaA region of the Bacillus subtilis genome journal March 2000
The CitST two-component system regulates the expression of the Mg-citrate transporter in Bacillus subtilis journal August 2000
The role of the CcpA transcriptional regulator in carbon metabolism in Bacillus subtilis journal January 1996
Regulation of the Bacillus subtilis Phosphotransacetylase Gene journal August 1999
A family of bacterial regulators homologous to Gal and Lac repressors. journal August 1992
Carbon catabolite repression in bacteria: many ways to make the most out of nutrients journal August 2008
Regulation of the transport system for C4-dicarboxylic acids in Bacillus subtilis journal February 2000
Evaluation and characterization of catabolite-responsive elements (cre) of Bacillus subtilis journal March 2000
Involvement of Two Distinct Catabolite-Responsive Elements in Catabolite Repression of the Bacillus subtilis myo-Inositol (iol) Operon journal October 2001
Crystal Structure of the Lactose Operon Repressor and Its Complexes with DNA and Inducer journal March 1996
Site-directed mutagenesis of a catabolite repression operator sequence in Bacillus subtilis. journal August 1990
The 1.9 Å resolution structure of phospho-serine 46 HPr from Enterococcus faecalis 1 1Edited by P. Wright journal November 2000
Antitermination by GlpP, catabolite repression via CcpA and inducer exclusion triggered by P~GlpK dephosphorylation control Bacillus subtilis glpFK expression journal February 2002
Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization journal April 2002
DNA curvature and flexibility in vitro and in vivo journal February 2010
Quantification of the Influence of HPrSer46P on CcpA–cre Interaction journal May 2002
cAMP does not have an important role in carbon catabolite repression of the Escherichia coli lac operon journal February 2009
Residues His-15 and Arg-17 of HPr Participate Differently in Catabolite Signal Processing via CcpA journal January 2007
Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization journal April 2002
The Whole Lactose Repressor journal March 1996
Transcriptional Activation of the Bacillus subtilis ackA Gene Requires Sequences Upstream of the Promoter journal November 1998
Catabolite Regulation of the pta Gene as Part of Carbon Flow Pathways in Bacillus subtilis journal November 1999
Transcriptional Activation of the Bacillus subtilis ackA Promoter Requires Sequences Upstream of the CcpA Binding Site journal April 2001
Regulation of sigL Expression by the Catabolite Control Protein CcpA Involves a Roadblock Mechanism in Bacillus subtilis: Potential Connection between Carbon and Nitrogen Metabolism journal October 2005
CcpA Causes Repression of the phoPR Promoter through a Novel Transcription Start Site, PA6 journal February 2006
CcpA-Dependent Carbon Catabolite Repression in Bacteria journal December 2003
Fluorescence polarization analysis of protein-DNA and protein-protein interactions. journal June 1996

Cited By (12)

The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum journal June 2017
Elimination of carbon catabolite repression in Clostridium acetobutylicum—a journey toward simultaneous use of xylose and glucose journal May 2015
A Novel Dual- cre Motif Enables Two-Way Autoregulation of CcpA in Clostridium acetobutylicum journal April 2018
Probing the role of intercalating protein sidechains for kink formation in DNA journal February 2018
A Flexible Binding Site Architecture Provides New Insights into CcpA Global Regulation in Gram-Positive Bacteria journal March 2017
Regulation of carbohydrate degradation pathways in Pseudomonas involves a versatile set of transcriptional regulators journal April 2018
Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength journal January 2019
Comparative genomics and evolution of regulons of the LacI-family transcription factors journal June 2014
A metabolic checkpoint protein GlmR is important for diverting carbon into peptidoglycan biosynthesis in Bacillus subtilis journal September 2018
Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile journal September 2012
Data on publications, structural analyses, and queries used to build and utilize the AlloRep database journal September 2016
Probing the regulatory effects of specific mutations in three major binding domains of the pleiotropic regulator CcpA of Bacillus subtilis journal October 2015

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