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Entry M0126    1.12.2.1    cytochrome-c3 hydrogenase

Next Step

Step 01

Dihydrogen coordinates to the Ni(II) centre, and a single electron is transferred from Ni(II) to the electron acceptor through the iron-sulfur clusters.

GIF of Reaction Step M0126.stg01


Comment: Hydrogen molecules diffuse from the surface of the protein and this is unlikely to be rate-limiting. Hydrogen easily permeates the protein and moves preferentially in channels to the Ni side of the active site. [1]. In this first step, a single electron is transferred from the Ni centre, and hydrogen binds, however, it is not yet clear whether the hydrogen molecule binds to the Ni or Fe centres. We have chosen to depict the initial binding at the Ni centre, as this is the side at which the hydrogen channel terminates, and work by Jayapal et al. suggests that this position is more likely [2].



Mechanisms

Coordination
Electron Transfer

Mechanism Components

Overall Reactant Used
Cofactor Used
Bond Formation
Metal Coordination
Intermediate Formation

Amino acids involved in the reaction step.

Amino Acid Location of Function Activity Function
Arg463B Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Ser486B Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Cys530B Side Chain spectator Metal Ligand
Cys65B Side Chain spectator Metal Ligand
Activator
Cys533B Side Chain spectator Metal Ligand
Activator
Electrostatic Stabiliser
Cys68B Side Chain spectator Metal Ligand
Activator
Electrostatic Stabiliser
His72B Side Chain spectator Hydrogen Bond Donor
Electrostatic Stabiliser
Glu18B Side Chain spectator Not Active

Metal Cofactors involved in Step 01

Metal Type Metal Identity Chain Activity Function
iron FCO 537 L spectator
iron F3S 266 S spectator
iron SF4 265 S spectator
nickel NI 538 L spectator
iron SF4 267 S spectator

Reactive Centre

Bonds Formed Bonds Cleaved Bonds Changed in Order Atom Types Involved
Ni-H
None
None
H
Ni

View similar reactions in MACiE.


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