Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.8 kDa 
• Atom Count: 4,892 
• Modelled Residue Count: 510 
• Deposited Residue Count: 510 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1B97

ANALYSIS OF A MUTATIONAL HOT-SPOT IN THE ECORV RESTRICTION ENDONUCLEASE: A CATALYTIC ROLE FOR A MAIN CHAIN CARBONYL GROUP

• PDB DOI:  https://doi.org/10.2210/pdb1B97/pdb
• NDB: PD0040

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-02-19 Released: 1999-02-26 
• Deposition Author(s): Thomas, M.P., Halford, S.E., Brady, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 

Literature

Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group.

Thomas, M.P., Brady, R.L., Halford, S.E., Sessions, R.B., Baldwin, G.S.

(1999) Nucleic Acids Res 27: 3438-3445

• PubMed: 10446231 
• DOI: https://doi.org/10.1093/nar/27.17.3438
• Primary Citation of Related Structures:  
  1B94, 1B95, 1B96, 1B97


• PubMed Abstract: 
  

Following random mutagenesis of the Eco RV endonuclease, a high proportion of the null mutants carry substitutions at Gln69. Such mutants display reduced rates for the DNA cleavage step in the reaction pathway, yet the crystal structures of wild-type Eco RV fail to explain why Gln69 is crucial for activity. In this study, crystal structures were determined for two mutants of Eco RV, with Leu or Glu at residue 69, bound to specific DNA. The structures of the mutants are similar to the native protein and no function can be ascribed to the side chain of the amino acid at this locus. Instead, the structures of the mutant proteins suggest that the catalytic defect is due to the positioning of the main chain carbonyl group. In the enzyme-substrate complex for Eco RV, the main chain carbonyl of Gln69 makes no interactions with catalytic functions but, in the enzyme-product complex, it coordinates a metal ion bound to the newly liberated 5'-phosphate. This re-positioning may be hindered in the mutant proteins. Molecular dynamics calculations indicate that the metal on the phosphoryl oxygen interacts with the carbonyl group upon forming the pentavalent intermediate during phosphodiester hydrolysis. A main chain carbonyl may thus play a role in catalysis by Eco RV.

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Organizational Affiliation: 

Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RESTRICTION ENDONUCLEASE ECORV	C [auth A], D [auth B]	244	Escherichia coli	Mutation(s): 1  Gene Names: ecoRVR EC: 3.1.21.4
UniProt
Find proteins for P04390 (Escherichia coli) Explore P04390  Go to UniProtKB:  P04390

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3')	A [auth C], B [auth D]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.279 
• R-Value Work: 0.219 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.651	α = 96.65
b = 49.224	β = 108.91
c = 64.039	γ = 107.53

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-26 
Deposition Author(s): Thomas, M.P., Halford, S.E., Brady, R.L.

Revision History  

• Version 1.0: 1999-02-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references