2J08

Thermus DNA photolyase with 8-Iod-riboflavin antenna chromophore

• PDB DOI: https://doi.org/10.2210/pdb2J08/pdb

• Classification: LYASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-01 Released: 2007-05-01 
• Deposition Author(s): Klar, T., Kaiser, G., Hennecke, U., Carell, T., Batschauer, A., Essen, L.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.256 
• R-Value Work: 0.163 
• R-Value Observed: 0.167 

Literature

Natural and Non-Natural Antenna Chromophores in the DNA Photolyase from Thermus Thermophilus

Klar, T., Kaiser, G., Hennecke, U., Carell, T., Batschauer, A., Essen, L.-O.

(2006) Chembiochem 7: 1798

• PubMed: 17051659 
• DOI: https://doi.org/10.1002/cbic.200600206
• Primary Citation of Related Structures:  
  2J07, 2J08, 2J09


• PubMed Abstract: 
  

  X-ray crystallographic and functional analysis of the class I DNA photolyase from Thermus thermophilus revealed the binding of flavin mononucleotide (FMN) as an antenna chromophore. The binding mode of FMN closely coincides with the binding of a deazaflavin-like chromophore in the related class I DNA photolyase from Anacystis nidulans. Compared to the R46E mutant, which lacks a conserved arginine in the binding site for the antenna chromophore, the FMN-comprising holophotolyase exhibits an eightfold higher activity at 450 nm. The facile incorporation of the flavin cofactors 8-hydroxy-deazariboflavin and 8-iodo-8-demethyl-riboflavin into the binding site for the antenna chromophore paves the way for wavelength-tuning of the activity spectra of DNA photolyases by using synthetic flavins.

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Organizational Affiliation: 

Philipps-Universität Marburg, Fachbereich Chemie, Hans-Meerwein-Strasse, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.51 kDa 
• Atom Count: 3,572 
• Modelled Residue Count: 419 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYRIBODIPYRIMIDINE PHOTO-LYASE	A	420	Thermus thermophilus HB8	Mutation(s): 0  EC: 4.1.99.3
UniProt
Find proteins for P61497 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P61497  Go to UniProtKB:  P61497

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
IRF	E [auth A]	1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO-3,4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)-D-RIBITOL C16 H17 I N4 O6 GXUZMSUHTJJUNU-LOWVWBTDSA-N
PO4	F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.256 
• R-Value Work: 0.163 
• R-Value Observed: 0.167 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.62	α = 90
b = 112.62	β = 90
c = 140.262	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Klar, T., Kaiser, G., Hennecke, U., Carell, T., Batschauer, A., Essen, L.-O.

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-07-05
  Changes: Data collection
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description