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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];  [2];  [3];  [4];  [2]
  1. Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center. Dept. of Biochemistry and Molecular Biology; DOE/OSTI
  2. Univ. of Texas, Houston, TX (United States). MD Anderson Cancer Center. Dept. of Biochemistry and Molecular Biology
  3. Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen (Germany). Institut fur Biologie. Lehrstuhl fur Mikrobiologie
  4. 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:
University 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, Journal Name: Nucleic Acids Research Journal Issue: 7 Vol. 39; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (12)

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

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