3EYY | pdb_00003eyy

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

• PDB DOI: https://doi.org/10.2210/pdb3EYY/pdb

• Classification: TRANSPORT
• Organism(s): Streptomyces coelicolor
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.264 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

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

• PubMed: 19336416 
• DOI: https://doi.org/10.1093/nar/gkp198
• Primary Citation 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. 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.

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

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: 33.49 kDa 
• Atom Count: 2,088 
• Modeled Residue Count: 266 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative iron uptake regulatory protein	A, B	145	Streptomyces coelicolor	Mutation(s): 0
UniProt
Find proteins for Q9K4F8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9K4F8  Go to UniProtKB:  Q9K4F8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	J [auth A], K [auth A], R [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
ZN	D [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	C [auth A], L [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A], F [auth A], G [auth A], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.264 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.164	α = 90
b = 79.164	β = 90
c = 49.732	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations