3LX4

Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG)

Summary for 3LX4

• Entry DOI: 10.2210/pdb3lx4/pdb
• Descriptor: Fe-hydrogenase, IRON/SULFUR CLUSTER, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: hydrogenase, hyda, hydrogen, h-cluster, [4fe-4s] cluster, iron-sulfur cluster, insertion, biosynthesis, maturation, intermediate, evolution, oxidoreductase
• Biological source: Chlamydomonas reinhardtii
• Total number of polymer chains: 2
• Total formula weight: 99624.45

Authors

Mulder, D.W.,Boyd, E.S.,Sarma, R.,Lange, R.K.,Endrizzi, J.A.,Broderick, J.B.,Peters, J.W. (deposition date: 2010-02-24, release date: 2010-04-28, Last modification date: 2023-09-06)

Primary citation

Mulder, D.W.,Boyd, E.S.,Sarma, R.,Lange, R.K.,Endrizzi, J.A.,Broderick, J.B.,Peters, J.W.
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG).
Nature, 465:248-251, 2010

PubMed Abstract: Complex enzymes containing Fe-S clusters are ubiquitous in nature, where they are involved in a number of fundamental processes including carbon dioxide fixation, nitrogen fixation and hydrogen metabolism. Hydrogen metabolism is facilitated by the activity of three evolutionarily and structurally unrelated enzymes: the [NiFe]-hydrogenases, [FeFe]-hydrogenases and [Fe]-hydrogenases (Hmd). The catalytic core of the [FeFe]-hydrogenase (HydA), termed the H-cluster, exists as a [4Fe-4S] subcluster linked by a cysteine thiolate to a modified 2Fe subcluster with unique non-protein ligands. The 2Fe subcluster and non-protein ligands are synthesized by the hydrogenase maturation enzymes HydE, HydF and HydG; however, the mechanism, synthesis and means of insertion of H-cluster components remain unclear. Here we show the structure of HydA(DeltaEFG) (HydA expressed in a genetic background devoid of the active site H-cluster biosynthetic genes hydE, hydF and hydG) revealing the presence of a [4Fe-4S] cluster and an open pocket for the 2Fe subcluster. The structure indicates that H-cluster synthesis occurs in a stepwise manner, first with synthesis and insertion of the [4Fe-4S] subcluster by generalized host-cell machinery and then with synthesis and insertion of the 2Fe subcluster by specialized hydE-, hydF- and hydG-encoded maturation machinery. Insertion of the 2Fe subcluster presumably occurs through a cationically charged channel that collapses following incorporation, as a result of conformational changes in two conserved loop regions. The structure, together with phylogenetic analysis, indicates that HydA emerged within bacteria most likely from a Nar1-like ancestor lacking the 2Fe subcluster, and that this was followed by acquisition in several unicellular eukaryotes.

PubMed: 20418861
DOI: 10.1038/nature08993

Experimental method

X-RAY DIFFRACTION (1.97 Å)