4RH1

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spore photoproduct lyaseA368Geobacillus thermodenitrificans NG80-2Mutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0TT (Subject of Investigation/LOI)
Query on 0TT

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
EEM (Subject of Investigation/LOI)
Query on EEM

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 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], I [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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 = 53.44α = 90
b = 58.56β = 90
c = 130.96γ = 90
Software Package:
Software NamePurpose
HEIDIdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references