1TEZ

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair

Mees, A., Klar, T., Gnau, P., Hennecke, U., Eker, A.P.M., Carell, T., Essen, L.-O.

(2004) Science 306: 1789-1793

  • DOI: 10.1126/science.1101598

  • PubMed Abstract: 

    • DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degree ...

    DNA photolyases use light energy to repair DNA that comprises ultraviolet-induced lesions such as the cis-syn cyclobutane pyrimidine dimers (CPDs). Here we report the crystal structure of a DNA photolyase bound to duplex DNA that is bent by 50 degrees and comprises a synthetic CPD lesion. This CPD lesion is flipped into the active site and split there into two thymines by synchrotron radiation at 100 K. Although photolyases catalyze blue light-driven CPD cleavage only above 200 K, this structure apparently mimics a structural substate during light-driven DNA repair in which back-flipping of the thymines into duplex DNA has not yet taken place.

    Related Citations: 
    • Crystal Structure of DNA Photolyase from Anacystis
      Tamada, T.,Kitadokoro, K.,Higuchi, Y.,Inaka, K.,Yasui, A.,De Ruiter, P.E.,Eker, A.P.,Miki, K.
      (1997) Nat.Struct.Mol.Biol. 4: 887

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, Butenandt-Strasse 5-13, Ludwig Maximilians University, D-81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Deoxyribodipyrimidine photolyase
A, B, C, D
474Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)Mutation(s): 0 
Gene Names: phr (phrA)
EC: 4.1.99.3
Find proteins for P05327 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Go to UniProtKB:  P05327
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'I,K11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'J,L9N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*C)-3'M,O4N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(P*GP*CP*CP*GP*A)-3'N,P5N/A
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
C
Query on C
Download SDF File 
Download CCD File 
I, K
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
HDF
Query on HDF
Download SDF File 
Download CCD File 
A, B, C, D
8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE
C16 H17 N3 O7
AUEILLWDYUBWCM-AGIUHOORSA-N
 Ligand Interaction
MG
Query on MG
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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TCP
Query on TCP
Download SDF File 
Download CCD File 
I, K
5'-METHYLTHYMIDINE
C11 H16 N2 O5
KTCKNHCDUKONFQ-DJLDLDEBSA-N
 Ligand Interaction
G
Query on G
Download SDF File 
Download CCD File 
I, K
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TCP
Query on TCP
I, K
DNA LINKINGC11 H16 N2 O5DT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.815α = 90.00
b = 88.505β = 90.11
c = 161.622γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CCP4data scaling
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2018-05-30
    Type: Advisory, Data collection, Derived calculations