5H3R | pdb_00005h3r

Crystal Structure of mutant MarR C80S from E.coli complexed with operator DNA

• PDB DOI: https://doi.org/10.2210/pdb5H3R/pdb
• NAKB: 5H3R

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-10-26 Released: 2017-08-02 
• Deposition Author(s): Zhu, R., Lou, H., Hao, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator.

Zhu, R., Hao, Z., Lou, H., Song, Y., Zhao, J., Chen, Y., Zhu, J., Chen, P.R.

(2017) J Biol Inorg Chem 22: 685-693

• PubMed: 28124121 
• DOI: https://doi.org/10.1007/s00775-017-1442-7
• Primary Citation Related Structures: 
  5H3R


• PubMed Abstract: 
  

  Multiple antibiotic resistance regulator (MarR) family proteins are widely conserved transcription factors that control bacterial resistance to antibiotics, environmental stresses, as well as the regulation of virulence determinants. Escherichia coli MarR, the prototype member of this family, has recently been shown to undergo copper(II)-catalyzed inter-dimer disulfide bond formation via a unique cysteine residue (Cys80) residing in its DNA-binding domain. However, despite extensive structural characterization of the MarR family proteins, the structural mechanism for DNA binding of this copper(II)-sensing MarR factor remains elusive. Here, we report the crystal structures of DNA-bound forms of MarR, which revealed a unique, concerted generation of two new helix-loop-helix motifs that facilitated MarR's DNA binding. Structural analysis and electrophoretic mobility shift assays (EMSA) show that the flexibility of Gly116 in the center of helix α5 and the extensive hydrogen-bonding interactions at the N-terminus of helix α1 together assist the reorientation of the wHTH domains and stabilize MarR's DNA-bound conformation.

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Organizational Affiliation: 
• Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. [e-mail].
Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.59 kDa 
• Atom Count: 3,070 
• Modeled Residue Count: 323 
• Deposited Residue Count: 336 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Multiple antibiotic resistance protein MarR	C [auth A], D [auth B]	147	Escherichia coli K-12	Mutation(s): 1  Gene Names: marR, cfxB, inaR, soxQ, b1530, JW5248
UniProt
Find proteins for P27245 (Escherichia coli (strain K12)) Explore P27245  Go to UniProtKB:  P27245

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*AP*CP*TP*TP*GP*CP*CP*TP*GP*GP*GP*CP*AP*AP*TP*AP*TP*T)-3')	A [auth C]	21	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*AP*TP*AP*TP*TP*GP*CP*CP*CP*AP*GP*GP*CP*AP*AP*GP*TP*AP*T)-3')	B [auth D]	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.435	α = 90
b = 67.435	β = 90
c = 219.951	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Zhu, R., Lou, H., Hao, Z.

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description