Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.74 kDa 
• Atom Count: 10914 
• Residue Count: 1245 
• Unique protein chains: 1

1XJE

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex

• DOI: 10.2210/pdb1XJE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-09-23 Released: 2005-10-11 
• Deposition Author(s): Larsson, K.-M., Jordan, A., Eliasson, R., Reichard, P., Logan, D.T., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.

Larsson, K.-M., Jordan, A., Eliasson, R., Reichard, P., Logan, D.T., Nordlund, P.

(2004) Nat Struct Mol Biol 11: 1142-1149

• PubMed: 15475969 
• DOI: 10.1038/nsmb838
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained primarily through the regulation of the RNR substrate specificity. Here, the molecular mechanism of the allosteric substrate specificity regulation is revealed through the structures of a dimeric coenzyme B12-dependent RNR from Thermotoga maritima, both in complexes with four effector-substrate nucleotide pairs and in three complexes with only effector. The mechanism is based on the flexibility of loop 2, a key structural element, which forms a bridge between the specificity effector and substrate nucleotides. Substrate specificity is achieved as different effectors and their cognate substrates stabilize specific discrete loop 2 conformations. The mechanism of substrate specificity regulation is probably general for most class I and class II RNRs.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ribonucleotide reductase, B12-dependent	A, B	644	Thermotoga maritima	Mutation(s): 0  Gene Names: nrdJ EC: 1.17.4.1
Find proteins for O33839 (Thermotoga maritima) Explore O33839  Go to UniProtKB:  O33839

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	A, B	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
GDP	A, B	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.391	α = 90
b = 124.376	β = 103.68
c = 107.243	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-23 
• Released Date: 2005-10-11 
Deposition Author(s): Larsson, K.-M., Jordan, A., Eliasson, R., Reichard, P., Logan, D.T., Nordlund, P.

Revision History 

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description