1BGB | pdb_00001bgb

ECORV ENDONUCLEASE COMPLEX WITH 5'-CGGGATATCCC DNA

• PDB DOI: https://doi.org/10.2210/pdb1BGB/pdb
• NAKB: 1BGB

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


• Deposited: 1998-05-28 Released: 1998-10-28 
• Deposition Author(s): Perona, J., Horton, N.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.246 (Depositor) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.

Horton, N.C., Perona, J.J.

(1998) J Biological Chem 273: 21721-21729

• PubMed: 9705308 
• DOI: https://doi.org/10.1074/jbc.273.34.21721
• Primary Citation Related Structures: 
  1BGB


• PubMed Abstract: 
  

  The 2.1-A cocrystal structure of EcoRV endonuclease bound to 5'-CGGGATATCCC, in a crystal lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined, shows novel base recognition in the major groove of the DNA flanking the GATATC target site. Lys104 of the enzyme interacts through water molecules with the exocyclic N-4 amino groups of flanking cytosines. Steric exclusion of water molecule-binding sites by the 5-methyl group of thymine drives the adoption of alternative water-mediated contacts with AT versus GC flanks. This structure provides a rare example of structural adaptability in the recognition of different DNA sequences by a protein and suggests preferred strategies for the expansion of target site specificity by EcoRV.

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Organizational Affiliation: 
• Department of Chemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, California 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: 63.79 kDa 
• Atom Count: 4,264 
• Modeled Residue Count: 486 
• Deposited Residue Count: 510 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ECORV ENDONUCLEASE	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(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3')	A [auth C], B [auth D]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.246 (Depositor) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.4	α = 96
b = 50.2	β = 109
c = 64.1	γ = 108

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-28 
Deposition Author(s): Perona, J., Horton, N.C.

Revision History  

• Version 1.0: 1998-10-28
  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: 2024-02-07
  Changes: Data collection, Database references