1TEZ

COMPLEX BETWEEN DNA AND THE DNA PHOTOLYASE FROM ANACYSTIS NIDULANS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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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
  • Primary Citation of Related Structures:  
    1TEZ

  • 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 degrees and comprises a synthetic CPD lesion ...

    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 Biol 4: 887
    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyribodipyrimidine photolyaseI [auth A],
J [auth B],
K [auth C],
L [auth D]		474Synechococcus elongatus PCC 6301Mutation(s): 0 
Gene Names: phr, phrA, syc1392_c
EC: 4.1.99.3
UniProt
Find proteins for P05327 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Explore P05327 
Go to UniProtKB:  P05327
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05327
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*AP*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3'A [auth I],
C [auth K]		11N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(P*CP*GP*AP*AP*GP*CP*CP*GP*A)-3'B [auth J],
D [auth L]		9N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*TP*CP*GP*C)-3'E [auth M],
G [auth O]		4N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
5'-D(P*GP*CP*CP*GP*A)-3'F [auth N],
H [auth P]		5N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
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AA [auth C],
CA [auth D],
V [auth A],
Y [auth B]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
HDF
Query on HDF
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BA [auth C],
DA [auth D],
W [auth A],
Z [auth B]		8-HYDROXY-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL)-5-DEAZAISOALLOXAZINE
C16 H17 N3 O7
AUEILLWDYUBWCM-AGIUHOORSA-N		 Ligand Interaction
G
Query on G
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O [auth I],
S [auth K]		GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N		 Ligand Interaction
C
Query on C
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N [auth I],
P [auth I],
R [auth K],
T [auth K]		CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N		 Ligand Interaction
TCP
Query on TCP
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M [auth I],
Q [auth K]		5'-METHYLTHYMIDINE
C11 H16 N2 O5
KTCKNHCDUKONFQ-DJLDLDEBSA-N		 Ligand Interaction
MG
Query on MG
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U [auth A],
X [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.815α = 90
b = 88.505β = 90.11
c = 161.622γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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