6BXK

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and MTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 

Starting Model: experimental
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Literature

Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.

Dong, M.Kathiresan, V.Fenwick, M.K.Torelli, A.T.Zhang, Y.Caranto, J.D.Dzikovski, B.Sharma, A.Lancaster, K.M.Freed, J.H.Ealick, S.E.Hoffman, B.M.Lin, H.

(2018) Science 359: 1247-1250

  • DOI: https://doi.org/10.1126/science.aao6595
  • Primary Citation of Related Structures:  
    6BXK, 6BXL, 6BXM, 6BXN, 6BXO

  • PubMed Abstract: 

    Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-(3-amino-3-carboxypropyl)histidine synthase
A, B
378Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: dph2PH1105
EC: 2.5.1.108
UniProt
Find proteins for O58832 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58832 
Go to UniProtKB:  O58832
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58832
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.509α = 90
b = 80.458β = 90
c = 161.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description