Subsystem: Hydrogenases
This subsystem's description is:
This SS is not complete and is in a process of development. It is not a trivial task to distinguish and to annotate properly all variety of hydrogenases.
Here we are giving a short overview which we use as a guide line in our annotation process.
Thirty sequenced microbial hydrogenases are classified into six classes according to sequence homologies, metal content and physiological function. The first class contains nine H2-uptake membrane-bound NiFe-hydrogenases from eight aerobic, facultative anaerobic and anaerobic bacteria. The second comprises four periplasmic and two membrane-bound H2-uptake NiFe(Se)-hydrogenases from sulphate-reducing bacteria.
The third consists of four periplasmic Fe-hydrogenases from strict anaerobic bacteria. The fourth contains eight methyl-viologen- (MV), factor F420- (F420) or NAD-reducing soluble hydrogenases from methanobacteria and Alcaligenes eutrophusH16. The fifth is the H2-producing labile hydrogenase isoenzyme 3 of Escherichia coli. The sixth class contains two soluble tritium-exchange hydrogenases of cyanobacteria. The results of sequence comparison reveal that the 30 hydrogenases have evolved from at least three different ancestors. While those of class I, II, IV and V hydrogenases are homologous, i.e. sharing the same evolutionary origin, both class III and VI hydrogenases are neither related to each other nor to the other classes. Sequence comparison scores, hierarchical cluster structures and phylogenetic trees show that class II falls into two distinct clusters composed of NiFe- and NiFeSe-hydrogenases, respectively. These results also reveal that class IV comprises three distinct clusters: MV-reducing, F420-reducing and NAD-reducing hydrogenases. Specific signatures of the six classes of hydrogenases as well as some subclusters have been detected. Analyses of motif compositions indicate that all hydrogenases, except those of class VI, must contain some common motifs probably participating in the formation of hydrogen activation domains and electron transfer domains. The regions of hydrogen activation domains are highly conserved and can be divided into two categories. One corresponds to the 'nickel active center' of NiFe(Se)-hydrogenases. It consists of two possible specific nickel-binding motifs, RxCGxCxxxH and DPCxxCxxH, located at the N- and C-termini of so-called large subunits in the dimeric hydrogenases, respectively. The other is the H-cluster of the Fe-hydrogenases. It might comprise three motifs on the C-terminal half of the large subunits. However, the motifs corresponding to the putative electron transfer domains, as well as their polypeptides chains, are poorly or even not at all conserved. They are present essentially on the small subunits in NiFe-hydrogenases. Some of these motifs resemble the typical ferredoxin-like Fe-S cluster binding site.
For more information, please check out the description and the additional notes tabs, below
| Diagram | Functional Roles | Subsystem Spreadsheet | Description | Additional Notes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Oops! We thought there was a diagram here, but we can't find it. Sorry
This SS is not complete and is in a process of development. It is not a trivial task to distinguish and to annotate properly all variety of hydrogenases. Here we are giving a short overview which we use as a guide line in our annotation process. Thirty sequenced microbial hydrogenases are classified into six classes according to sequence homologies, metal content and physiological function. The first class contains nine H2-uptake membrane-bound NiFe-hydrogenases from eight aerobic, facultative anaerobic and anaerobic bacteria. The second comprises four periplasmic and two membrane-bound H2-uptake NiFe(Se)-hydrogenases from sulphate-reducing bacteria. The third consists of four periplasmic Fe-hydrogenases from strict anaerobic bacteria. The fourth contains eight methyl-viologen- (MV), factor F420- (F420) or NAD-reducing soluble hydrogenases from methanobacteria and Alcaligenes eutrophusH16. The fifth is the H2-producing labile hydrogenase isoenzyme 3 of Escherichia coli. The sixth class contains two soluble tritium-exchange hydrogenases of cyanobacteria. The results of sequence comparison reveal that the 30 hydrogenases have evolved from at least three different ancestors. While those of class I, II, IV and V hydrogenases are homologous, i.e. sharing the same evolutionary origin, both class III and VI hydrogenases are neither related to each other nor to the other classes. Sequence comparison scores, hierarchical cluster structures and phylogenetic trees show that class II falls into two distinct clusters composed of NiFe- and NiFeSe-hydrogenases, respectively. These results also reveal that class IV comprises three distinct clusters: MV-reducing, F420-reducing and NAD-reducing hydrogenases. Specific signatures of the six classes of hydrogenases as well as some subclusters have been detected. Analyses of motif compositions indicate that all hydrogenases, except those of class VI, must contain some common motifs probably participating in the formation of hydrogen activation domains and electron transfer domains. The regions of hydrogen activation domains are highly conserved and can be divided into two categories. One corresponds to the 'nickel active center' of NiFe(Se)-hydrogenases. It consists of two possible specific nickel-binding motifs, RxCGxCxxxH and DPCxxCxxH, located at the N- and C-termini of so-called large subunits in the dimeric hydrogenases, respectively. The other is the H-cluster of the Fe-hydrogenases. It might comprise three motifs on the C-terminal half of the large subunits. However, the motifs corresponding to the putative electron transfer domains, as well as their polypeptides chains, are poorly or even not at all conserved. They are present essentially on the small subunits in NiFe-hydrogenases. Some of these motifs resemble the typical ferredoxin-like Fe-S cluster binding site. HybF is homologous to Zn finger protein HypA/HybF (possibly regulating hydrogenase expression). HypA, hypB-hydrogenase expression/maturation proteins F420-reducing hydrogenase is homologous to NADH-reducing hydrogenase from Cyanobacteria,NADH-red hydrog. maturation factor occures in F420-hydrogenase related cluster in Magnetospirillum as wel. HyfB is homologous to Formate hydrogenlyase subunit 3 HyfC is homologous to Formate hydrogenlyase subunit 4 HyfE no homology to any dehydrogenase subunits HyfG is homologous to Formate hydrogenlyase subunit 5 Hyfh is homologous to Formate hydrogenlyase subunit 6 Coenzyme F420-reducing hydrogenase related protein-probably folate byosynthesis. C2?-included as a potential candidate for cytochrome subunit of hydrogenase in Desulfovibrio HyaF=part of HoxQ ??Honology to one of HoxQ termini Ni,Fe-hydrogenase III large subunit and small subunit and Fe-S hydrogenase conmponents I and II seem to be parts of formate dehydrogenase multisubunit complex (positional clustering). Useful information to follow while annotating hydrogenases (from Wu LF, Mandrand MA. 1993,Microbial hydrogenases: primary structure, classification, signatures and phylogeny.FEMS Microbiol Rev.10(3-4):243-69. Review.): Cyanobacteria: From: Journal of Bacteriology, March 2004, p. 1737-1746, Vol. 186, No. 6 Sustained Photoevolution of Molecular Hydrogen in a Mutant of Synechocystis sp. Strain PCC 6803 Deficient in the Type I NADPH-Dehydrogenase Complex Laurent Cournac,1 Geneviève Guedeney,1 Gilles Peltier,1 and Paulette M. Vignais2 The Synechocystis reversible hydrogenase is a pentameric [NiFe] enzyme utilizing NAD(P) as a substrate (4, 34). The HoxY and HoxH subunits form the [NiFe]hydrogenase moiety, while three other subunits (HoxU, HoxF, and HoxE), homologous to subunits of complex I of respiratory chains, contain NAD(P), flavin mononucleotide, and FeS binding sites (3, 6, 18, 33, 34; also reviewed in reference 44). Since no hydrogenase activity has been found in a hydrogenase deletion mutant ({Delta}hoxH), it has been concluded that in Synechocystis sp. strain PCC 6803 only the bidirectional HoxEFUYH hydrogenase functions for H2 uptake or H2 production (2). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
