• Prosthetic group features
• Reactions catalysed by hydrogenase
• The properties of the Fe-S clusters
• Fe hydrogenase in enzyme databases
• Fe hydrogenase in motif databases
• Fe hydrogenase in alignment databases
• Fe hydrogenase in 3­D databases
• References

Centre	Prosthetic group	Formal oxidation/ spin states
H	Clostridium pasteurianum [Fe2(S2X)CY](CY)4(H2O)[Fe4S4](SCys)4 X = H2O or ?; Y = O or N	[Fe4S4]+ (S=1/2)¶; [Fe4S4]2+ (S=0) ¶ Antiferromagnetically coupled to [Fe2] (S=1/2) subcluster FeII-FeII (S=0 or S=1); FeII-FeIII (S=1/2)|; FeIII-FeIII (S=1/2)| | Antiferromagnetically coupled to [Fe4S4]+ subcluster
	Desulfovibrio desulfuricans [Fe2{S-(CH2)3-S}X](CY)4[Fe4S4](SCys)4 X = OH¯ or H2O; Y = O or N
FS4A FS4B	[Fe4S4](SCys)4	[Fe4S4]+ (S=1/2); [Fe4S4]2+ (S=0)
FS4C	Clostridium pasteurianum [Fe4S4](SCys)3NHis	[Fe4S4]+ (admixed S=1/2, S=3/2); [Fe4S4]2+ (S=0)
FS2	Clostridium pasteurianum [Fe2S2](SCys)4	[Fe2S2]+ (S=1/2); [Fe2S2]2+ (S=0)

Hydrogenases catalyse the reversible oxidation of molecular hydrogen (H₂) and play a vital role in anaerobic metabolism. Metal­containing hydrogenases are subdivided into three classes: Fe hydrogenases, Ni-Fe hydrogenases and Ni-Fe-Se hydrogenases [1]. Hydrogen oxidation is coupled to the reduction of electron acceptors such as oxygen, nitrate, sulphate, carbon dioxide and fumarate, whereas proton reduction (H₂ evolution) is essential in pyruvate fermentation or in the disposal of excess electrons.

The hydrogenases containing no other metal than Fe are called Fe hydrogenases (Fe-Hases), also known as "Fe-only" hydrogenases. Two families of Fe-Hases are recognised: (I) cytoplasmic, soluble, monomeric Fe-Hases, found in strict anaerobes such as Clostridium pasteurianum and Megasphaera elsdenii. They are extremely sensitive to inactivation by O₂ and catalyse both H₂ evolution (1) and uptake (2); and (II) periplasmic, heterodimeric Fe-Hases from Desulfovibrio spp., which can be purified aerobically and catalyse mainly H₂ oxidation [2]. Cytochrome c₃ and cytochrome c₆ act as physiological electron donors D or acceptors A for Fe-Hases [3]:

2H+ + Dred H2 + Dox	(1)
H2 + Aox 2H+ + Ared	(2)

3­D structures of H₂ evolving Fe-Hase I from Clostridium pasteurianum (CpI) and Desulfovibrio desulfuricans uptake hydrogenase (DdH) are known [4, 5]. The overall structure of CpI resembles a mushroom consisting of four domains: the large active site domain forms "cap" and three smaller domains form "stem". The "stem" domains bind four iron-sulphur clusters and are termed FS4A-FS4B, FS4C and FS2. The N­terminal FS2 domain binds a [Fe₂S₂] cluster and share the overall fold with plant­type ferredoxins. The FS4A-FS4B domain is adjacent to the active site domain; it contains two [Fe₄S₄] clusters and has the overall fold similar to that of bacterial­type 2×[Fe₄S₄] ferredoxins. The FS4C domain is placed between the FS2 and FS4A-FS4B domains and consists of two ­helices linked by a loop that binds a single [Fe₄S₄] cluster via one His and three Cys residues. The large subunit of DdH lacks FS4C and FS2 clusters and corresponding domains. The small subunit of DdH has an unusual fold consisting of alternating random coil and four ­helices that form a "belt" around the large subunit.

The active site domain of the Fe-Hases contains an unusual Fe-S centre termed the H­cluster [2]. H­cluster consists of the [Fe₄S₄] subcluster bridged via the Cys thiolate to the [Fe₂] (binuclear iron) subcluster. The two iron atoms are designated Fe1 and Fe2 (proximal and distal with respect to the [Fe₄S₄] subcluster) and are ~2.6 Å apart. With the exception of bridging Cys, the diiron subcluster is coordinated by non­protein ligands. In CpI, both iron atoms are octahedrally coordinated to five CO/CN ligands, three S ligands and one water molecule. Fe1 and Fe2 are bridged by two S atoms and one CO or CN ligand. The two bridging sulphurs themselves are bridged by atom(s) of unknown identity. In DdH, Fe1 and Fe2 are bridged by a small molecule that has been modelled as 1,3­propanedithiol (PDT). Fe1 is octahedrally coordinated while Fe2 has square pyramidal coordination geometry. Some ligand coordination properties of the metal centres of the two Fe-Hases are summarised in the following table (see corresponding references for details of active site distances):

Enzyme	[Fe2S2] cluster ligands	[Fe4S4] clusters ligands			H­cluster ligands			Ref.
		FS4C	FS4B	FS4A	[Fe4S4] subcluster	[Fe2] subcluster
						Fe1	Fe2
Clostridium pasteurianum hydrogenase (CpI)	Cys33; Cys46; Cys49; Cys62	His94; Cys98; Cys101; Cys107	Cys147; Cys150; Cys153; Cys200	Cys157; Cys190; Cys193; Cys196	Cys300; Cys355; Cys499	2×CY (Y = O or N)	H2O; 2×CY (Y = O or N)	[4]
						2×µ­S¯; µ­CY (Y = O or N)
					µ­S(Cys503)
	<-- 11 Å -->			<-- 9 Å -->		<-- 2.62 Å -->
	<-- 17 Å -->		<-- 10 Å -->		<-- ~5 Å -->
		<-- 8 Å -->
Desulfovibrio desulfuricans hydrogenase (DdH)	-	Cys35; Cys38; Cys41; Cys76	Cys45; Cys66; Cys69; Cys72	-	Cys179; Cys234; Cys378	CO; CN¯	CO; CN¯	[5]
						µ­S-(CH2)3-µ­S; µ­X (X = OH¯ or H2O)
					µ­S(Cys382)

Iron hydrogenase in enzyme databases

ENZYME	LIGAND	BRENDA	Official name	Alternative name
1.18.99.1	1.18.99.1	1.18.99.1	Hydrogenase	Hydrogenlyase

Iron hydrogenase in motif databases

PRINTS ID	PRINTS AC	PROSITE/BLOCKS ID	PROSITE AC	BLOCKS AC
4FE4SFRDOXIN	PR00353	4FE4S_FERREDOXIN	PS00198	BL00198

Iron hydrogenase in alignment databases

Protein Superfamily	Pfam	LPFC 3­D alignment
00176; hydrogenase (Fe) large chain	PF00037; fer4	-
00178; hydrogenase (Fe) small chain	-	-

Iron hydrogenase in 3­D databases

PDB	scop	BSM	RELI Base	Header	¹
1feh	-	1feh	-	Fe-only hydrogenase; Clostridium pasteurianum	-

¹ Macromolecular Structures abstract. Full text is available to BioMedNet Members

References

1. Fauque, G., Peck, H.D., Jr., Moura, J.J.G., Huynh, B.­H., Berlier, Y., DerVartanian, D.V., Teixeira, M., Przybyla, A.E., Lespinat, P.A., Moura, I. and LeGall, J. (1988) The three classes of hydrogenases from sulfate­reducing bacteria of the genus Desulfovibrio. FEMS Microbiol. Rev. 4, 299-344.
2. Adams, M.W.W. (1990) The structure and mechanism of iron­hydrogenases. Biochim. Biophys. Acta 1020, 115-145.
3. Pereira, I.A.C., Romão, C.V., Xavier, A.V., LeGall, J. and Teixeira, M. (1998) Electron transfer between hydrogenases and mono­ and multiheme cytochromes in Desulfovibrio ssp. J. Biol. Inorg. Chem. 3, 494-498.
4. Peters, J.W., Lanzilotta, W.N., Lemon, B.J. and Seefeldt, L.C. (1998) X­ray crystal structure of the Fe­only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 282, 1853-1858.
5. Nicolet, Y., Piras, C., Legrand, P., Hatchikian, E.C. and Fontecilla­Camps, J.C. (1999) Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. Structure 7, 13-23.

Bibliography on structural studies of iron hydrogenases

Reviews on iron hydrogenases