PDBsum entry 4xdd

Oxidoreductase

PDB id: 4xdd

Contents

Protein chains

582 a.a.

Ligands

SF4 ×8

FES ×2

GOL ×3

Metals

_CL ×4

_MG ×4

Waters ×1400

PDB id:

4xdd

Name:

Oxidoreductase

Title:

Apo [fefe]-hydrogenase cpi

Structure:

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

Source:

Clostridium pasteurianum. Organism_taxid: 1501. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.60Å R-factor: 0.145 R-free: 0.166

Authors:

J.Esselborn,E.Hofmann,G.Kurisu,T.Happe

Key ref:

J.Esselborn et al. (2016). A structural view of synthetic cofactor integration into [FeFe]-hydrogenases. Chem Sci, 7, 959-968. PubMed id: 29896366

Date:

19-Dec-14 Release date: 11-Nov-15

Protein chains

P29166  (PHF1_CLOPA) -  Iron hydrogenase 1 from Clostridium pasteurianum

Seq: 574 a.a.

Struc: 582 a.a.

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

Chem Sci 7:959-968 (2016)

PubMed id: 29896366

A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.

J.Esselborn, N.Muraki, K.Klein, V.Engelbrecht, N.Metzler-Nolte, U.P.Apfel, E.Hofmann, G.Kurisu, T.Happe.

ABSTRACT

[FeFe]-hydrogenases are nature's fastest catalysts for the evolution or oxidation of hydrogen. Numerous synthetic model complexes for the [2Fe] subcluster (2Fe_H) of their active site are known, but so far none of these could compete with the enzymes. The complex Fe₂[μ-(SCH₂)₂X](CN)₂(CO)₄^2- with X = NH was shown to integrate into the apo-form of [FeFe]-hydrogenases to yield a fully active enzyme. Here we report the first crystal structures of the apo-form of the bacterial [FeFe]-hydrogenase CpI from Clostridium pasteurianum at 1.60 Å and the active semisynthetic enzyme, CpI^ADT, at 1.63 Å. The structures illustrate the significant changes in ligand coordination upon integration and activation of the [2Fe] complex. These changes are induced by a rigid 2Fe_H cavity as revealed by the structure of apoCpI, which is remarkably similar to CpI^ADT. Additionally we present the high resolution crystal structures of the semisynthetic bacterial [FeFe]-hydrogenases CpI^PDT (X = CH₂), CpI^ODT (X = O) and CpI^SDT (X = S) with changes in the headgroup of the dithiolate bridge in the 2Fe_H cofactor. The structures of these inactive enzymes demonstrate that the 2Fe_H-subcluster and its protein environment remain largely unchanged when compared to the active enzyme CpI^ADT. As the active site shows an open coordination site in all structures, the absence of catalytic activity is probably not caused by steric obstruction. This demonstrates that the chemical properties of the dithiolate bridge are essential for enzyme activity.