1BSU

STRUCTURAL AND ENERGETIC ORIGINS OF INDIRECT READOUT IN SITE-SPECIFIC DNA CLEAVAGE BY A RESTRICTION ENDONUCLEASE

• PDB DOI: https://doi.org/10.2210/pdb1BSU/pdb
• NAKB: 1BSU

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-08-30 Released: 1998-09-09 
• Deposition Author(s): Perona, J.J., Martin, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease.

Martin, A.M., Sam, M.D., Reich, N.O., Perona, J.J.

(1999) Nat Struct Biol 6: 269-277

• PubMed: 10074946 
• DOI: https://doi.org/10.1038/6707
• Primary Citation of Related Structures:  
  1BSU, 1BUA


• PubMed Abstract: 
  

  Specific recognition by EcoRV endonuclease of its cognate, sharply bent GATATC site at the center TA step occurs solely via hydrophobic interaction with thymine methyl groups. Mechanistic kinetic analyses of base analog-substituted DNAs at this position reveal that direct readout provides 5 kcal mol(-1) toward specificity, with an additional 6-10 kcal mol(-1) arising from indirect readout. Crystal structures of several base analog complexes show that the major-groove hydrophobic contacts are crucial to forming required divalent metal-binding sites, and that indirect readout operates in part through the sequence-dependent free-energy cost of unstacking the center base-pair step of the DNA.

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Organizational Affiliation: 

Department of Chemistry, University of California at Santa Barbara, 93106-9510, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.6 kDa 
• Atom Count: 4,281 
• Modelled Residue Count: 486 
• Deposited Residue Count: 509 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDONUCLEASE ECORV (3.1.21.4)	C [auth A], D [auth B]	244	Escherichia coli	Mutation(s): 0  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(P*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3')	A [auth C]	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*GP*AP*(5CM)P*IP*TP*CP*TP*T)-3')	B [auth D]	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.3	α = 109.1
b = 64	β = 108.1
c = 49.1	γ = 96.5

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-09-09 
Deposition Author(s): Perona, J.J., Martin, A.M.

Revision History  

• Version 1.0: 1998-09-09
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-20
  Changes: Derived calculations
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description