| Literature References | 1. FAUQUE, G., PECK, H.D., 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.
The three classes of hydrogenases from sulfate-reducing bacteria of the
genus Desulfovibrio.
FEMS MICROBIOL.REV. 4 299-344 (1988).
2. CAMMACK, R., FERNANDEZ, V.M. AND HATCHIKIAN, E.C.
Nickel-iron hydrogenase.
METHODS ENZYMOL. 243 43-68 (1994).
3. PRZYBYLA, A.E., ROBBINS, J., MENON, N. AND PECK, H.D.
Structure-function relationships among the nickel-containing hydrogenases.
FEMS MICROBIOL.REV. 8 109-135 (1992).
4. VOLBEDA, A., CHARON, M.H., PIRAS, C., HATCHIKIAN, E.C., FREY, M.
AND FONTECILLA-CAMPS, J.C.
Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas.
NATURE 373 580-587 (1995).
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| Documentation | Hydrogenases catalyse the reversible oxidation of molecular hydrogen and
play a vital role in anaerobic metabolism. Metal-containing hydrogenases
are subdivided into three classes: Fe (`iron only') 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 (hydrogen evolution)
is essential in pyruvate fermentation or in the disposal of excess electrons.
The Ni-Fe hydrogenases, when isolated, are found to catalyse both hydrogen
evolution and uptake, with low-potential multihaem cytochromes, such as
cytochrome c3, acting as either electron donors or acceptors, depending on
their oxidation state [2]. Both periplasmic (soluble) and membrane-bound
hydrogenases are known.
The Ni-Fe hydrogenases are heterodimeric proteins consisting of small (S)
and large (L) subunits. The small subunit contains three iron-sulphur
clusters (two [4Fe-4S] and one [3Fe-4S]); the large subunit contains a
nickel ion [2,3]. Small subunits of membrane-bound Ni-Fe hydrogenases
contain a C-terminal domain of about 40 residues that is absent in
periplasmic forms.
The 3D structure of the Ni-Fe hydrogenase from Desulfovibrio gigas has been
determined at 2.85A resolution [4]. The small subunit consists of two
domains, I(S) and II(S). The alpha/beta twisted open sheet structure of the
N-terminal I(S) domain is similar to that of flavodoxin; the C-terminal
II(S) domain contains two alpha-helices and has no beta-structure. The Fe-S
clusters are distributed almost along a straight line, with the [3Fe-4S]
cluster located half-way between the two [4Fe-4S] clusters. The two [4Fe-4S]
clusters have been termed proximal (prox) and distal (dist), based on their
distance to the Ni atom. Domain I(S) binds the [4Fe-4S]prox cluster, while
domain II(S) binds the [4Fe-4S]dist and [3Fe-4S] clusters. The [4Fe-4S]prox
cluster is coordinated by Cys-17, Cys-20, Cys-112 and Cys-148; [4Fe-4S]dist
is coordinated by His-185, Cys-188, Cys-213 and Cys-219; and [3Fe-4S] is
coordinated by Cys-228, Cys-246 and Cys-249. [4Fe-4S]dist is the first known
example of a [4Fe-4S] cluster in protein structure ligated by a His side
chain. A crown of acidic residues surrounds the partially-exposed His-185
and this might provide a recognition site for the redox partner (cytochrome
c3) [4]. A mechanism of electron transfer from the Ni active site through
the Fe-S clusters to the cytochrome c3 has been suggested [4]. The role of
the [3Fe-4S] cluster is not clear: its high redox potential and its absence
from some homologous hydrogenases put its involvement in electron transfer
in doubt [4].
NIHGNASESMLL is an 11-element fingerprint that provides a signature for the
small subunit of Ni-Fe hydrogenases. The fingerprint was derived from an
initial alignment of 12 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length - motifs 1-6 span the
I(S) domain and motifs 7-11 span the II(S) domain. Motif 1 includes two
invariant Cys residues that bind [4Fe-4S]prox; motifs 5 and 6 each include
a conserved Cys, which contribute to the [4Fe-4S]prox cluster; motif 8
includes the conserved His and Cys residues that bind [4Fe-4S]dist; motif 9
includes three invariant Cys residues, the first two of which bind
[4Fe-4S]dist, the third binding the [3Fe-4S] cluster; and motif 10 contains
two conserved Cys residues that contribute to the [3Fe-4S] cluster. Two
iterations on OWL28.1 were required to reach convergence, at which point a
true set comprising 21 sequences was identified. Several partial matches
were also found: PHSS_DESBA (which lacks motif 10) is a Ni-Fe-Se hydrogenase
containing only two Fe-S centres; ECU2837794 is an E.coli hydrogenase that
lacks motif 11; MMDNAVHT (lacking motifs 2, 5 and 11) and S49928 (lacking
motifs 2, 5, 7 and 11) are membrane-bound hydrogenases from Methanosarcina
mazei; DVUPNFHGA (lacking motifs 5-8), is a periplasmic Ni-Fe hydrogenase
from Desulfovibrio gigas; RCAHUPT1 (matching motifs 5-7 and 9), B49938
(matching motifs 5, 6 and 8) and RHBHUPUVA (matching 1, 5 and 6) are hupU
gene products; FRHG_METTH (matching motifs motifs 1, 4 and 6) is the gamma-
subunit of the nickel-containing 8-hydroxy-5-deazaflavin reducing
hydrogenase from Methanobacterium thermoautotrophicum; S24800, C30315,
D30315 and MBFMVRH2 (all matching only motifs 4 and 6), are methyl
viologen-reducing hydrogenase gamma-subunits.
An update on SPTR37_9f identified a true set of 22 sequences, and 12
partial matches.
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