4U63

Crystal structure of a bacterial class III photolyase from Agrobacterium tumefaciens at 1.67A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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This is version 1.2 of the entry. See complete history


Literature

The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways.

Scheerer, P.Zhang, F.Kalms, J.von Stetten, D.Krau, N.Oberpichler, I.Lamparter, T.

(2015) J Biol Chem 290: 11504-11514

  • DOI: 10.1074/jbc.M115.637868
  • Primary Citation of Related Structures:  
    4U63

  • PubMed Abstract: 
  • Photolyases are proteins with an FAD chromophore that repair UV-induced pyrimidine dimers on the DNA in a light-dependent manner. The cyclobutane pyrimidine dimer class III photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors ...

    Photolyases are proteins with an FAD chromophore that repair UV-induced pyrimidine dimers on the DNA in a light-dependent manner. The cyclobutane pyrimidine dimer class III photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. Here we present the crystal structure of a class III photolyase termed photolyase-related protein A (PhrA) of Agrobacterium tumefaciens at 1.67-Å resolution. PhrA contains 5,10-methenyltetrahydrofolate (MTHF) as an antenna chromophore with a unique binding site and mode. Two Trp residues play pivotal roles for stabilizing MTHF by a double π-stacking sandwich. Plant cryptochrome I forms a pocket at the same site that could accommodate MTHF or a similar molecule. The PhrA structure and mutant studies showed that electrons flow during FAD photoreduction proceeds via two Trp triads. The structural studies on PhrA give a clearer picture on the evolutionary transition from photolyase to photoreceptor.


    Organizational Affiliation

    the Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany, tilman.lamparter@kit.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA photolyaseA498Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: Atu1218phrA
EC: 4.1.99.3
UniProt
Find proteins for A9CJC9 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CJC9 
Go to UniProtKB:  A9CJC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CJC9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MHF
Query on MHF

Download Ideal Coordinates CCD File 
B [auth A]5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
C20 H23 N7 O6
QYNUQALWYRSVHF-OLZOCXBDSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
R [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.867α = 90
b = 81.867β = 90
c = 195.952γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2015-05-13
    Changes: Database references