5YHZ

Structure of Lactococcus lactis ZitR, E41A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation.

Zhu, R.Song, Y.Liu, H.Yang, Y.Wang, S.Yi, C.Chen, P.R.

(2017) Proc Natl Acad Sci U S A 114: 13661-13666

  • DOI: 10.1073/pnas.1708563115
  • Primary Citation of Related Structures:  
    5YHY, 5YHX, 5YHZ, 5YI0, 5YI2, 5YI1, 5YI3

  • PubMed Abstract: 
  • Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here w ...

    Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here we show that the MarR-type zinc transcriptional regulator ZitR switches one of its histidine nitrogen atoms for zinc coordination during the allosteric control of DNA binding. The Zn(II)-coordination nitrogen on histidine 42 within ZitR's high-affinity zinc site (site 1) switches from Nε2 to Nδ1 upon Zn(II) binding to its low-affinity zinc site (site 2), which facilitates ZitR's conversion from the nonoptimal to the optimal DNA-binding conformation. This histidine switch-mediated cooperation between site 1 and site 2 enables ZitR to adjust its DNA-binding affinity in response to a broad range of zinc fluctuation, which may allow the fine tuning of transcriptional regulation.


    Organizational Affiliation

    Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc transport transcriptional regulatorA146Lactococcus lactis subsp. lactis Il1403Mutation(s): 1 
Gene Names: zitRL168265
Find proteins for Q9CDU5 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q9CDU5 
Go to UniProtKB:  Q9CDU5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.357α = 90
b = 94.238β = 110.1
c = 31.915γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Foundation of ChinaChina2010CB912302 2012CB917301
National Natural Science Foundation of ChinaChina21225206 91013005 21001010
E-Institutes of Shanghai Municipal Education CommissionChinaE09013

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references