8X9H | pdb_00008x9h

Crystal structure of CO dehydrogenase mutant (F41C)

• PDB DOI: https://doi.org/10.2210/pdb8X9H/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Carboxydothermus hydrogenoformans Z-2901
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-30 Released: 2024-04-17 
• Deposition Author(s): Lee, H.H., Heo, Y., Yoon, H.J., Kim, S.M., Kong, S.Y.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.142 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

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

• PubMed: 38548760 
• DOI: https://doi.org/10.1038/s41467-024-46909-1
• Primary Citation 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.

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Organizational Affiliation: 
• School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea. [e-mail].
School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea.
Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea. [e-mail].
School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea. [e-mail].
Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan, 44919, Republic of Korea. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.11 kDa 
• Atom Count: 5,024 
• Modeled Residue Count: 633 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase 2	A	656	Carboxydothermus hydrogenoformans Z-2901	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XCC	D [auth A]	FE(4)-NI(1)-S(4) CLUSTER Fe4 Ni S4 QGLWBXDZIHZONR-UHFFFAOYSA-N
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	C [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
FE	E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.142 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.281	α = 90
b = 75.39	β = 111.18
c = 70.792	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Lee, H.H., Heo, Y., Yoon, H.J., Kim, S.M., Kong, S.Y.

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Funding Organization	Location	Grant Number
Other government	Korea, Republic Of	--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Database references
• Version 1.2: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Data collection, Derived calculations, Structure summary