5D8C image
Entry Detail
PDB ID:
5D8C
Title:
Crystal structure of HiNmlR, a MerR family regulator lacking the sensor domain, bound to promoter DNA
Biological Source:
PDB Version:
Deposition Date:
2015-08-17
Release Date:
2016-06-29
Method Details:
Experimental Method:
Resolution:
2.25 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:MerR family regulator protein
Chain IDs:A, B
Chain Length:137
Number of Molecules:2
Biological Source:Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*TP*CP*AP*CP*TP*CP*TP*AP*AP*G)-3')
Chain IDs:C
Chain Length:18
Number of Molecules:1
Biological Source:Haemophilus influenzae Rd KW20
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*TP*TP*AP*GP*AP*GP*TP*GP*AP*AP*CP*TP*CP*TP*AP*AP*G)-3')
Chain IDs:D
Chain Length:18
Number of Molecules:1
Biological Source:Haemophilus influenzae Rd KW20
Primary Citation
Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region.
Nucleic Acids Res. 44 6981 6993 (2016)
PMID: 27307602 DOI: 10.1093/nar/gkw543

Abstact

Pathogenic bacteria such as Haemophilus influenzae, a major cause of lower respiratory tract diseases, must cope with a range of electrophiles generated in the host or by endogenous metabolism. Formaldehyde is one such compound that can irreversibly damage proteins and DNA through alkylation and cross-linking and interfere with redox homeostasis. Its detoxification operates under the control of HiNmlR, a protein from the MerR family that lacks a specific sensor region and does not bind metal ions. We demonstrate that HiNmlR is a thiol-dependent transcription factor that modulates H. influenzae response to formaldehyde, with two cysteine residues (Cys54 and Cys71) identified to be important for its response against a formaldehyde challenge. We obtained crystal structures of HiNmlR in both the DNA-free and two DNA-bound forms, which suggest that HiNmlR enhances target gene transcription by twisting of operator DNA sequences in a two-gene operon containing overlapping promoters. Our work provides the first structural insights into the mechanism of action of MerR regulators that lack sensor regions.

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