PDBsum entry 6yf4

Oxidoreductase

PDB id: 6yf4

Contents

Protein chains

580 a.a.

Ligands

402 ×2

SF4 ×8

FES ×2

Metals

_MG ×3

Waters ×903

PDB id:

6yf4

Name:

Oxidoreductase

Title:

[Fefe]-hydrogenase i from clostridium pasteurianum (cpi), variant e279d

Structure:

Iron hydrogenase 1. Chain: a, b. Synonym: cpi,fe-only hydrogenase,[fe] hydrogenase. Engineered: yes. Mutation: yes

Source:

Clostridium pasteurianum. Organism_taxid: 1501. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: delta-iscr

Resolution:

1.77Å R-factor: 0.200 R-free: 0.234

Authors:

J.Duan,E.Hofmann,T.Happe

Key ref:

O.Lampret et al. (2020). The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases. Proc Natl Acad Sci U S A, 117, 20520-20529. PubMed id: 32796105 DOI: 10.1073/pnas.2007090117

Date:

25-Mar-20 Release date: 02-Sep-20

Protein chains

P29166  (PHF1_CLOPA) -  Iron hydrogenase 1 from Clostridium pasteurianum

Seq: 574 a.a.

Struc: 580 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.12.7.2 - ferredoxin hydrogenase.
• Reaction: H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 reduced [2Fe-2S]-[ferredoxin] + 2 H⁺
• Cofactor: Iron-sulfur; Ni(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1073/pnas.2007090117

Proc Natl Acad Sci U S A 117:20520-20529 (2020)

PubMed id: 32796105

The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases.

O.Lampret, J.Duan, E.Hofmann, M.Winkler, F.A.Armstrong, T.Happe.

ABSTRACT

As paradigms for proton-coupled electron transfer in enzymes and benchmarks for a fully renewable H₂ technology, [FeFe]-hydrogenases behave as highly reversible electrocatalysts when immobilized on an electrode, operating in both catalytic directions with minimal overpotential requirement. Using the [FeFe]-hydrogenases from Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA1) we have conducted site-directed mutagenesis and protein film electrochemistry to determine how efficient catalysis depends on the long-range coupling of electron and proton transfer steps. Importantly, the electron and proton transfer pathways in [FeFe]-hydrogenases are well separated from each other in space. Variants with conservative substitutions (glutamate to aspartate) in either of two positions in the proton-transfer pathway retain significant activity and reveal the consequences of slowing down proton transfer for both catalytic directions over a wide range of pH and potential values. Proton reduction in the variants is impaired mainly by limiting the turnover rate, which drops sharply as the pH is raised, showing that proton capture from bulk solvent becomes critical. In contrast, hydrogen oxidation is affected in two ways: by limiting the turnover rate and by a large overpotential requirement that increases as the pH is raised, consistent with the accumulation of a reduced and protonated intermediate. A unique observation having fundamental significance is made under conditions where the variants still retain sufficient catalytic activity in both directions: An inflection appears as the catalytic current switches direction at the 2H⁺/H₂ thermodynamic potential, clearly signaling a departure from electrocatalytic reversibility as electron and proton transfers begin to be decoupled.