8X9H

Crystal structure of CO dehydrogenase mutant (F41C)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity.

Kim, S.M.Kang, S.H.Lee, J.Heo, Y.Poloniataki, E.G.Kang, J.Yoon, H.J.Kong, S.Y.Yun, Y.Kim, H.Ryu, J.Lee, H.H.Kim, Y.H.

(2024) Nat Commun 15: 2732-2732

  • DOI: https://doi.org/10.1038/s41467-024-46909-1
  • Primary Citation of Related Structures:  
    8X9D, 8X9E, 8X9F, 8X9G, 8X9H

  • PubMed Abstract: 

    Fe‒S cluster-harboring enzymes, such as carbon monoxide dehydrogenases (CODH), employ sophisticated artificial electron mediators like viologens to serve as potent biocatalysts capable of cleaning-up industrial off-gases at stunning reaction rates. Unraveling the interplay between these enzymes and their associated mediators is essential for improving the efficiency of CODHs. Here we show the electron mediator-interaction site on ChCODHs (Ch, Carboxydothermus hydrogenoformans) using a systematic approach that leverages the viologen-reactive characteristics of superficial aromatic residues. By enhancing mediator-interaction (R57G/N59L) near the D-cluster, the strategically tailored variants exhibit a ten-fold increase in ethyl viologen affinity relative to the wild-type without sacrificing the turn-over rate (k cat ). Viologen-complexed structures reveal the pivotal positions of surface phenylalanine residues, serving as external conduits for the D-cluster to/from viologen. One variant (R57G/N59L/A559W) can treat a broad spectrum of waste gases (from steel-process and plastic-gasification) containing O 2 . Decoding mediator interactions will facilitate the development of industrially high-efficient biocatalysts encompassing gas-utilizing enzymes.


  • Organizational Affiliation

    School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea. smkimlife@unist.ac.kr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase 2656Carboxydothermus hydrogenoformans Z-2901Mutation(s): 1 
Gene Names: cooS2
EC: 1.2.7.4
UniProt
Find proteins for Q9F8A8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901))
Explore Q9F8A8 
Go to UniProtKB:  Q9F8A8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F8A8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.281α = 90
b = 75.39β = 111.18
c = 70.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references