6FPI

Structure of fully reduced Hydrogenase (Hyd-1) variant E28Q

Summary for 6FPI

• Entry DOI: 10.2210/pdb6fpi/pdb
• Related: 5LMM
• Descriptor: Hydrogenase-1 small chain, SULFATE ION, Hydrogenase-1 large chain, ... (11 entities in total)
• Functional Keywords: nife hydrogenase, iron sulphur cluster, periplasm, hydrogen, oxidoreductase
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 4
• Total formula weight: 204687.69

Authors

Carr, S.B.,Armstrong, F.A.,Evans, R.M. (deposition date: 2018-02-09, release date: 2018-12-19, Last modification date: 2024-01-17)

Primary citation

Evans, R.M.,Ash, P.A.,Beaton, S.E.,Brooke, E.J.,Vincent, K.A.,Carr, S.B.,Armstrong, F.A.
Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase.
J. Am. Chem. Soc., 140:10208-10220, 2018

PubMed Abstract: Catalytic long-range proton transfer in [NiFe]-hydrogenases has long been associated with a highly conserved glutamate (E) situated within 4 Å of the active site. Substituting for glutamine (Q) in the O-tolerant [NiFe]-hydrogenase-1 from Escherichia coli produces a variant (E28Q) with unique properties that have been investigated using protein film electrochemistry, protein film infrared electrochemistry, and X-ray crystallography. At pH 7 and moderate potential, E28Q displays approximately 1% of the activity of the native enzyme, high enough to allow detailed infrared measurements under steady-state conditions. Atomic-level crystal structures reveal partial displacement of the amide side chain by a hydroxide ion, the occupancy of which increases with pH or under oxidizing conditions supporting formation of the superoxidized state of the unusual proximal [4Fe-3S] cluster located nearby. Under these special conditions, the essential exit pathway for at least one of the H ions produced by H oxidation, and assumed to be blocked in the E28Q variant, is partially repaired. During steady-state H oxidation at neutral pH (i.e., when the barrier to H exit via Q28 is almost totally closed), the catalytic cycle is dominated by the reduced states "Ni-R" and "Ni-C", even under highly oxidizing conditions. Hence, E28 is not involved in the initial activation/deprotonation of H, but facilitates H exit later in the catalytic cycle to regenerate the initial oxidized active state, assumed to be Ni-SI. Accordingly, the oxidized inactive resting state, "Ni-B", is not produced by E28Q in the presence of H at high potential because Ni-SI (the precursor for Ni-B) cannot accumulate. The results have important implications for understanding the catalytic mechanism of [NiFe]-hydrogenases and the control of long-range proton-coupled electron transfer in hydrogenases and other enzymes.

PubMed: 30070475
DOI: 10.1021/jacs.8b04798

Experimental method

X-RAY DIFFRACTION (1.5 Å)