4RH1

Spore photoproduct lyase C140A/S76C mutant with bound AdoMet and dinucleoside spore photoproduct

• PDB DOI: https://doi.org/10.2210/pdb4RH1/pdb

• Classification: LYASE
• Organism(s): Geobacillus thermodenitrificans NG80-2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-10-01 Released: 2014-10-22 
• Deposition Author(s): Benjdia, A., Heil, K., Winkler, A., Carell, T., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.325 
• R-Value Work: 0.264 
• R-Value Observed: 0.267 

Literature

Rescuing DNA repair activity by rewiring the H-atom transfer pathway in the radical SAM enzyme, spore photoproduct lyase.

Benjdia, A., Heil, K., Winkler, A., Carell, T., Schlichting, I.

(2014) Chem Commun (Camb) 50: 14201-14204

• PubMed: 25285338 
• DOI: https://doi.org/10.1039/c4cc05158k
• Primary Citation of Related Structures:  
  4RH0, 4RH1


• PubMed Abstract: 
  

  The radical SAM enzyme, spore photoproduct lyase, requires an H-atom transfer (HAT) pathway to catalyze DNA repair. By rational engineering, we demonstrate that it is possible to rewire its HAT pathway, a first step toward the development of novel catalysts based on the radical SAM enzyme scaffold.

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Organizational Affiliation: 

Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.82 kDa 
• Atom Count: 2,943 
• Modelled Residue Count: 340 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spore photoproduct lyase	A	368	Geobacillus thermodenitrificans NG80-2	Mutation(s): 2  Gene Names: GTNG_2348 EC: 4.1.99.14
UniProt
Find proteins for A4IQU1 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IQU1  Go to UniProtKB:  A4IQU1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0TT	J [auth A]	1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-[[(5R)-1-[(2R,4S,5R)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-methyl-2,4-bis(oxidanylidene)-1,3-diazinan-5-yl]methyl]pyrimidine-2,4-dione C20 H28 N4 O10 WCJUEZCRTGBSQU-BZMYHREGSA-N
EEM	C [auth A]	[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium C15 H23 N6 O5 Se GGJFWMOVUFBSIN-FCKMPRQPSA-O
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.325 
• R-Value Work: 0.264 
• R-Value Observed: 0.267 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.44	α = 90
b = 58.56	β = 90
c = 130.96	γ = 90

Software Package:

Software Name	Purpose
HEIDI	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Benjdia, A., Heil, K., Winkler, A., Carell, T., Schlichting, I.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations