5ZR6 | pdb_00005zr6

Manganese-dependent transcriptional repressor complex with manganese

• PDB DOI: https://doi.org/10.2210/pdb5ZR6/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-23 Released: 2019-03-20 
• Deposition Author(s): Cong, X.Y., Xu, S.J., Wang, J.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.269 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Literature

Crystal structures of manganese-dependent transcriptional repressor MntR (Rv2788) from Mycobacterium tuberculosis in apo and manganese bound forms.

Cong, X.Y., Yuan, Z.L., Wang, Z., Wei, B., Xu, S.J., Wang, J.B.

(2018) Biochem Biophys Res Commun 501: 423-427

• PubMed: 29730293 
• DOI: https://doi.org/10.1016/j.bbrc.2018.05.005
• Primary Citation Related Structures: 
  5ZR4, 5ZR6


• PubMed Abstract: 
  

  The pathogenic Mycobacterium tuberculosis encodes two members of the DtxR family metalloregulators, IdeR and MntR. IdeR represses gene expression in response to ferrous iron, while MntR (Rv2788) functions as a manganese-dependent transcriptional repressor, which represses the expression of manganese transporter genes to maintain manganese homeostasis. Although the structural study towards IdeR is in-depth, there is no MntR structure available. Herein, we report both apo and manganese bound forms of MntR structures from M. tuberculosis. MntR has evolved into two metal ion binding sites like other DtxR proteins and for the first time, we captured the two sites fully occupied by its natural ions with one Mn ²⁺ ion at the first site and two Mn ²⁺ ions at the second binding site (binuclear manganese cluster). The conformation change of MntR resulting from manganese binding could prime the MntR for DNA binding, which is a conserved activation mechanism among DtxR family.

---

Organizational Affiliation: 
• State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China.
Shandong Asia-pacific Highharve Organisms Science and Technology, CO., LTD, China.
State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China. Electronic address: [e-mail].
State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.29 kDa 
• Atom Count: 3,286 
• Modeled Residue Count: 424 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-dependent transcriptional regulator	A, B	226	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: sirR, sirR_2
UniProt
Find proteins for I6Y1Q2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y1Q2  Go to UniProtKB:  I6Y1Q2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.269 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.12	α = 90
b = 47.459	β = 116.04
c = 88.468	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Cong, X.Y., Xu, S.J., Wang, J.B.

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations