{PDOC00400}
{PS00507; NI_HGENASE_L_1}
{PS00508; NI_HGENASE_L_2}
{BEGIN}
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* Nickel-dependent hydrogenases large subunit signatures *
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Hydrogenases are enzymes that catalyze the  reversible  activation of hydrogen
and which occur widely in prokaryotes as well as in some eukaryotes. There are
various types of hydrogenases,  but  all  of them seem to contain at least one
iron-sulfur cluster. They can be broadly divided into two groups: hydrogenases
containing nickel and, in  some cases,  also selenium (the [NiFe] and [NiFeSe]
hydrogenases) and those lacking nickel (the [Fe] hydrogenases).

The [NiFe] and [NiFeSe] hydrogenases  are  heterodimer that consist of a small
subunit that  contains  a  signal  peptide  and a large subunit. All the known
large subunits seem to be evolutionary related [1]; they contain  two Cys-x-x-
Cys motifs; one  at  their N-terminal end;  the other at their C-terminal end.
These four  cysteines  are  involved  in  the  binding  of  nickel [2]. In the
[NiFeSe] hydrogenases  the  first  cysteine  of  the  C-terminal  motif  is  a
selenocysteine which  has experimentally been shown to be a nickel ligand [3].
We have developed two patterns which are centered on the Cys-x-x-Cys motifs.

Alcaligenes eutrophus  possess  a NAD-reducing cytoplasmic  hydrogenase (hoxS)
[4]; this enzyme is composed of four subunits. Two of these subunits (beta and
delta) are responsible  for  the hydrogenase  reaction  and  are  evolutionary
related to the large and small subunits of membrane-bound hydrogenases.

The alpha  subunit  of  coenzyme  F420  hydrogenase  (EC 1.12.98.1) (FRH) from
archaebacterial methanogens also belongs to this family.

-Consensus pattern: R-G-[LIVMF]-E-x(15)-[QESMP]-[RK]-x-C-[GR]-[LIVM]-C
                    [The 2 C's are nickel ligands]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Consensus pattern: [FY]-D-[PI]-[CU]-[LIMAV]-[ASG]-C-x(2,3)-H
                    [The 2 C's are nickel ligands]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: January 2008 / Pattern updated.

[ 1] Menon N.K., Robbins J., Peck H.D. Jr., Chatelus C.Y., Choi E.-S.,
     Przybyla A.E.
     "Cloning and sequencing of a putative Escherichia coli [NiFe]
     hydrogenase-1 operon containing six open reading frames."
     J. Bacteriol. 172:1969-1977(1990).
     PubMed=2180913;
[ 2] Volbeda A., Charon M.-H., Piras C., Hatchikian E.C., Frey M.,
     Fontecilla-Camps J.C.
     "Crystal structure of the nickel-iron hydrogenase from Desulfovibrio
     gigas."
     Nature 373:580-587(1995).
     PubMed=7854413; DOI=10.1038/373580a0;
[ 3] Eidsness M.K., Scott R.A., Prickrill B., der Vartaninan D.V., LeGall J.,
     Moura I., Moura J.J.G., Peck H.D. Jr.
     "vidence for selenocysteine coordination to the active site nickel in
     the [NiFeSe]hydrogenases from Desulfovibrio baculatus."
     Proc. Natl. Acad. Sci. U.S.A. 86:147-151(1989).
     PubMed=2521386;
[ 4] Tran-Betcke A., Warnecke U., Boecker C., Zaborosch C., Friedrich B.
     "Cloning and nucleotide sequences of the genes for the subunits of
     NAD-reducing hydrogenase of Alcaligenes eutrophus H16."
     J. Bacteriol. 172:2920-2929(1990).
     PubMed=2188945;

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