Structure of Lactococcus lactis ZitR, wild type in complex with DNA

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report

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

    Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc transport transcriptional regulator146Lactococcus lactis subsp. lactis Il1403Mutation(s): 0 
Gene Names: zitRL168265
Find proteins for Q9CDU5 (Lactococcus lactis subsp. lactis (strain IL1403))
Explore Q9CDU5 
Go to UniProtKB:  Q9CDU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CDU5
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')16Lactococcus lactis
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth J]
CA [auth M]
DA [auth M]
EA [auth N]
AA [auth J],
BA [auth J],
CA [auth M],
DA [auth M],
EA [auth N],
FA [auth N],
Q [auth A],
R [auth A],
S [auth B],
T [auth B],
U [auth E],
V [auth E],
W [auth F],
X [auth F],
Y [auth I],
Z [auth I]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.616α = 90
b = 101.568β = 91.13
c = 101.544γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description