1H78

STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP.

• PDB DOI: https://doi.org/10.2210/pdb1H78/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-07-04 Released: 2002-07-04 
• Deposition Author(s): Larsson, K.-M., Andersson, J., Sjoeberg, B.-M., Nordlund, P., Logan, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 

Literature

Structural Basis for Allosteric Substrate Specificty Regulation in Anaerobic Ribonucleotide Reductase

Larsson, K.-M., Andersson, J., Sjoeberg, B.-M., Nordlund, P., Logan, D.T.

(2001) Structure 9: 739

• PubMed: 11587648 
• DOI: https://doi.org/10.1016/s0969-2126(01)00627-x
• Primary Citation of Related Structures:  
  1H78, 1H79, 1H7A, 1H7B


• PubMed Abstract: 
  

  The specificity of ribonucleotide reductases (RNRs) toward their four substrates is governed by the binding of deoxyribonucleoside triphosphates (dNTPs) to the allosteric specificity site. Similar patterns in the kinetics of allosteric regulation have been a strong argument for a common evolutionary origin of the three otherwise widely divergent RNR classes. Recent structural information settled the case for divergent evolution; however, the structural basis for transmission of the allosteric signal is currently poorly understood. A comparative study of the conformational effects of the binding of different effectors has not yet been possible; in addition, only one RNR class has been studied.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Stockholm University, S-106 91, Stockholm, Sweden.

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 PQS (software)

Macromolecule Content

• Total Structure Weight: 69.01 kDa 
• Atom Count: 4,371 
• Modelled Residue Count: 534 
• Deposited Residue Count: 605 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN	A	605	Tequatrovirus T4	Mutation(s): 1  EC: 1.17.4.2
UniProt
Find proteins for P07071 (Enterobacteria phage T4) Explore P07071  Go to UniProtKB:  P07071

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	B [auth A], C [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.254 
• R-Value Work: 0.221 
• R-Value Observed: 0.221 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.935	α = 90
b = 97.935	β = 90
c = 242.515	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-04 
Deposition Author(s): Larsson, K.-M., Andersson, J., Sjoeberg, B.-M., Nordlund, P., Logan, D.T.

Revision History  

• Version 1.0: 2002-07-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-01-17
  Changes: Atomic model, Data collection
• Version 2.1: 2018-10-24
  Changes: Data collection, Source and taxonomy
• Version 2.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description