3EYY

Structural basis for the specialization of Nur, a nickel-specific Fur homologue, in metal sensing and DNA recognition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition

An, Y.J.Ahn, B.-E.Han, A.-R.Kim, H.-M.Chung, K.M.Shin, J.-H.Cho, Y.-B.Roe, J.-H.Cha, S.-S.

(2009) Nucleic Acids Res 37: 3442-3451

  • DOI: 10.1093/nar/gkp198
  • Primary Citation of Related Structures:  
    3EYY

  • PubMed Abstract: 
  • Nur, a member of the Fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and anti-oxidative response in Streptomyces coelicolor. Here we report the 2.4-A resolution crystal structure of Nur. It contains a unique nickel-specific metal site in addition to a nonspecific common metal site ...

    Nur, a member of the Fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and anti-oxidative response in Streptomyces coelicolor. Here we report the 2.4-A resolution crystal structure of Nur. It contains a unique nickel-specific metal site in addition to a nonspecific common metal site. The identification of the 6-5-6 motif of the Nur recognition box and a Nur/DNA complex model reveals that Nur mainly interacts with terminal bases of the palindrome on complex formation. This contrasts with more distributed contacts between Fur and the n-1-n type of the Fur-binding motif. The disparity between Nur and Fur in the conformation of the S1-S2 sheet in the DNA-binding domain can explain their different DNA-recognition patterns. Furthermore, the fact that the specificity of Nur in metal sensing and DNA recognition is conferred by the specific metal site suggests that its introduction drives the evolution of Nur orthologs in the Fur family.


    Organizational Affiliation

    Marine and Extreme Genome Research Center, Korea Ocean Research & Development Institute, Ansan 426-744, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative iron uptake regulatory proteinA, B145Streptomyces coelicolorMutation(s): 0 
Find proteins for Q9K4F8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9K4F8 
Go to UniProtKB:  Q9K4F8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
J [auth A], K [auth A], R [auth B]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A], M [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], P [auth B], Q [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A], L [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], N [auth B], O [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.164α = 90
b = 79.164β = 90
c = 49.732γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2008-10-22 
  • Released Date: 2009-06-09 
  • Deposition Author(s): Cha, S.-S., An, Y.J.

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance