1DNP

STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of DNA photolyase from Escherichia coli.

Park, H.W.Kim, S.T.Sancar, A.Deisenhofer, J.

(1995) Science 268: 1866-1872


  • PubMed Abstract: 
  • Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr <> Pyr). The reaction is initiated by blue light and proceeds through long-range energy t ...

    Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr <> Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr <> Pyr dinucleotide, suggesting that the Pyr <> Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr <> Pyr occurs over van der Waals contact distance.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of Escherichia Coli DNA Photolyase
      Park, H.W.,Sancar, A.,Deisenhofer, J.
      (1993) J.Mol.Biol. 231: 1122


    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA PHOTOLYASE
A, B
471Escherichia coli (strain K12)Gene Names: phrB (phr)
EC: 4.1.99.3
Find proteins for P00914 (Escherichia coli (strain K12))
Go to UniProtKB:  P00914
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MHF
Query on MHF

Download SDF File 
Download CCD File 
A, B
5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
C20 H23 N7 O6
QYNUQALWYRSVHF-OLZOCXBDSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 62.600α = 99.10
b = 72.200β = 101.50
c = 58.500γ = 72.00
Software Package:
Software NamePurpose
XDSdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance