Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: EC:1.12.7.2 (hydrogenase)
 3,522 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We report on a computational investigation of the passive transport of H2 and O2 between the external solution and the hydrogen-producing active site of CpI [FeFe]-hydrogenase from Clostridium pasteurianum. Two distinct methodologies for studying gas access are discussed and applied: (1) temperature-controlled locally enhanced sampling, and (2) volumetric solvent accessibility maps, providing consistent results. Both methodologies confirm the existence and function of a previously hypothesized pathway and reveal a second major pathway that had not been detected by previous analyses of CpI's static crystal structure. Our results suggest that small hydrophobic molecules, such as H2 and O2, diffusing inside CpI, take advantage of well-defined preexisting packing defects that are not always apparent from the protein's static structure, but that can be predicted from the protein's dynamical motion. Finally, we describe two contrasting modes of intraprotein transport for H2 and O2, which in our model are differentiated only by their size.
Structure 2005 Sep
PMID:Finding gas diffusion pathways in proteins: application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects. 1615 89

Ech hydrogenase from Methanosarcina barkeri is a member of a distinct group of membrane-bound [NiFe] hydrogenases with sequence similarity to energy-conserving NADH:quinone oxidoreductase (complex I). The sequence of the enzyme predicts the binding of three [4Fe-4S] clusters, one by subunit EchC and two by subunit EchF. Previous studies had shown that two of these clusters could be fully reduced under 10(5) Pa of H2 at pH 7 giving rise to two distinct S1/2 electron paramagnetic resonance (EPR) signals, designated as the g = 1.89 and the g = 1.92 signal. Redox titrations at different pH values demonstrated that these two clusters had a pH-dependent midpoint potential indicating a function in ion pumping. To assign these signals to the subunits of the enzyme a set of M. barkeri mutants was generated in which seven of eight conserved cysteine residues in EchF were individually replaced by serine. EPR spectra recorded from the isolated mutant enzymes revealed a strong reduction or complete loss of the g = 1.92 signal whereas the g = 1.89 signal was still detectable as the major EPR signal in five mutant enzymes. It is concluded that the cluster giving rise to the g = 1.89 signal is the proximal cluster located in EchC and that the g = 1.92 signal results from one of the clusters of subunit EchF. The pH-dependence of these two [4Fe-4S] clusters suggests that they simultaneously mediate electron and proton transfer and thus could be an essential part of the proton-translocating machinery.
FEBS J 2005 Sep
PMID:Assignment of the [4Fe-4S] clusters of Ech hydrogenase from Methanosarcina barkeri to individual subunits via the characterization of site-directed mutants. 1615 94

The expression of many membrane bound [NiFe] hydrogenases is regulated by their substrate molecule, hydrogen. The HupSL hydrogenase, encoded in the hupSLCDHIR operon, probably plays a role in hydrogen recycling in the phototrophic purple bacterium, Thiocapsa roseopersicina BBS. RpoN, coding for sigma factor 54, was shown to be important for expression, suggesting a regulated biosynthsis from the hup gene cluster. The response regulator gene, hupR, has been identified in the hup operon and expression of hupSL was reduced in a chromosomal hupR mutant, which indicated that HupR was implicated in the activation process. The hupT and hupUV genes were isolated, and show similarity to the histidine kinase element of the H2-driven signal transduction system and to the regulatory hydrogenases of Ralstonia eutropha and Rhodobacter capsulatus, respectively. Although the genes of the entire H2 sensing and regulation system were present, the expression of the hupSL genes was not affected by the presence or absence of H2. Using reverse transcription PCR, we could not detect any mRNA specific to the hupTUV genes in cells grown under diverse conditions. The hupT and hupUV mutant strains had the same phenotype as the wild-type strains. The hupT gene product, expressed from a plasmid, repressed HupSL synthesis as expected while introduction of actively expressed hupTUV genes together derepressed the HupSL activity in T. roseopersicina. The gene product of hupUV behaves similarly to other regulatory hydrogenases and shows H-D exchange activity.
FEBS J 2005 Sep
PMID:Hydrogen independent expression of hupSL genes in Thiocapsa roseopersicina BBS. 1615 99

Escherichia coli requires nickel under anaerobic growth conditions for the synthesis of catalytically active NiFe hydrogenases. Transcription of the NikABCDE nickel transporter, which is required for NiFe hydrogenase synthesis, was previously shown to be upregulated by FNR (fumarate-nit rate regulator) in the absence of oxygen and repressed by the NikR repressor in the presence of high extracellular nickel levels. We present here a detailed analysis of nikABCDE transcriptional regulation and show that it closely correlates with hydrogenase expression levels. We identify a nitrate-dependent mechanism for nikABCDE repression that is linked to the NarLX two-component system. NikR is functional under all nickel conditions tested, but its activity is modulated by the total nickel concentration present as well as by one or more components of the hydrogenase assembly pathway. Unexpectedly, NikR function is independent of NikABCDE function, suggesting that NikABCDE is a hydrogenase-specific nickel transporter, consistent with its original identification as a hydrogenase (hyd) mutant. Further, the results suggest that the hydrogenase assembly pathway is sequestered within the cell. A second nickel import pathway in E. coli is implicated in NikR function.
J Bacteriol 2005 Sep
PMID:Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escherichia coli. 1615 64

By taking advantage of the tightly clustered genes for the membrane-bound [NiFe] hydrogenase of Ralstonia eutropha H16, broad-host-range recombinant plasmids were constructed carrying the entire membrane-bound hydrogenase (MBH) operon encompassing 21 genes. We demonstrate that the complex MBH biosynthetic apparatus is actively produced in hydrogenase-free hosts yielding fully assembled and functional MBH protein.
J Bacteriol 2005 Sep
PMID:Requirements for heterologous production of a complex metalloenzyme: the membrane-bound [NiFe] hydrogenase. 1615 96

Sulfur deprivation of algal cultures selectively and partially inactivates photosystem II (PSII)-catalyzed O(2) evolution, induces anaerobiosis and hydrogenase expression, and results in sustained H(2) photoproduction for several days. We show that re-addition of limiting amounts of sulfate (1-10 microM final concentration) to the cultures during the H(2)-production phase temporarily reactivates PSII photochemical and O(2)-evolution activity and re-establishes higher rates of electron transport through the photosynthetic electron transport chain. The reactivation of PSII occurs by de novo D1 protein synthesis, but does not result in the re-establishment of aerobic conditions in the reactor, detectable by dissolved-O(2) sensors. However, concomitant H(2) photoproduction is inhibited, possibly due to excessive intra-cellular levels of photosynthetically-evolved O(2). The partial recovery of electron transport rates correlates with the re-oxidation of the plastoquinone (PQ) pool, as observed by pulse-amplitude modulated (PAM) and fluorescence-induction measurements. These results show that the presence of a more oxidized PQ pool releases some of the down-regulation of electron transport caused by the anaerobic conditions.
Photosynth Res 2005 Sep
PMID:The effect of sulfur re-addition on H(2) photoproduction by sulfur-deprived green algae. 1617 Jun 32

Density functional theory has been used to investigate the reaction between H(2) and [Ni(NHPnPr(3))('S3')] or [Pd(NHPnPr(3))('S3')], where 'S3' = bis(2-sulfanylphenyl)sulfide(2-), which are among the few synthetic complexes featuring a metal coordination environment similar to that observed in the [NiFe] hydrogenase active site and capable of catalyzing H(2) heterolytic cleavage. Results allowed us to unravel the reaction mechanism, which is consistent with an oxidative addition-hydrogen migration pathway for [Ni(NHPnPr(3))('S3')], whereas metathesis is also possible with [Pd(NHPnPr(3))('S3')]. Unexpectedly, H(2) binding and activation implies structural reorganization of the metal coordination environment. It turns out that the structural rearrangement in [Ni(NHPnPr(3))('S3')] and [Pd(NHPnPr(3))('S3')] can take place due to the peculiar structural features of the Ni and Pd ligands, explaining the remarkable catalytic properties. However, the structural reorganization is the most unfavorable step along the H(2) cleavage pathway (DeltaG > 100 kJ mol(-1)), an observation that is relevant for the design and synthesis of novel biomimetic catalysts.
J Am Chem Soc 2005 Sep 28
PMID:DFT Investigation of H2 activation by [M(NHPnPr3)('S3')] (M = Ni, Pd). Insight into key factors relevant to the design of hydrogenase functional models. 1617 45

Uptake hydrogenase activity of Azospirillum brasilense in vitro (cell-free extract) was very much more sensitive to O(2) than was that of A. amazonense, and the O(2) pressure optima for uptake hydrogenase activities were 0.01 and 0.4 to 3 kPa for A. brasilense and A. amazonense, respectively. The addition of superoxide dismutase did not increase uptake hydrogenase activity of A. brasilense either in vivo or in vitro. The O(2) uptake rates of A. brasilense and A. amazonense were nearly the same. Inhibition of A. brasilense O(2)-dependent uptake hydrogenase activity by O(2) was highly reversible under the conditions tested. O(2) also markedly inhibited in vitro methylene blue-dependent uptake hydrogenase activity of A. brasilense, and this inhibition was highly reversible. It is concluded that the difference in O(2) tolerance of the uptake hydrogenases is not due to a difference in respiratory protection in the two species and may be due to inherent differences in the two enzymes. For the three species, A. brasilense, A. amazonense, and A. lipoferum, almost all the recovered methylene blue-dependent uptake hydrogenase activity was associated with the membrane fraction.
Appl Environ Microbiol 1989 Sep
PMID:Intracellular Location and O(2) Sensitivity of Uptake Hydrogenase in Azospirillum spp. 1634 11

Thirty-three strains of Bradyrhizobium japonicum within serogroup 110 were examined for genotypic diversity by using DNA-DNA hybridization analyses. The analysis of the DNA from 15 hydrogen-uptake-negative strains with the bradyrhizobial uptake hydrogenase probe pHU52 showed variation in degree of homology and restriction fragment length polymorphism of EcoRI-restricted DNA. Clustering analysis of the 33 strains on the basis of DNA-DNA hybridization analysis with four restriction enzymes and with the bradyrhizobial nodulation locus, pRJUT10, as probe indicated the existence of four groups of strains, which were less than 70% similar. Restriction digestion of genomic DNA with BamHI and DNA-DNA hybridization with pRJUT10 permitted classification of each of the strains according to a specific fingerprint pattern.
Appl Environ Microbiol 1993 Sep
PMID:Genotypic Diversity among Strains of Bradyrhizobium japonicum Belonging to Serogroup 110. 1634 53

Fukuyama, T. (University of Washington, Seattle), and E. J. Ordal. Induced biosynthesis of formic hydrogenlyase in iron-deficient cells of Escherichia coli. J. Bacteriol. 90:673-680. 1965.-Escherichia coli cells were grown aerobically on a lactate-mineral salts medium from which iron had been removed by extraction with 8-hydroxyquinoline and chloroform. These cells carried out induced biosynthesis of formic hydrogenlyase in a reaction mixture containing glucose, formate, and phosphate without the addition of amino acids, providing adequate amounts of iron salts were present. In the absence of iron, glucose was fermented and acids were produced, but no formic hydrogenlyase developed. When iron-deficient E. coli cells were repeatedly washed, the property of carrying out induced biosynthesis of formic hydrogenlyase with glucose, formate, phosphate, and iron was lost, but was restored on addition of acid-hydrolyzed casein to the reaction mixture. An energy source (provided as glucose) was necessary for enzyme production. Iron-deficient cells were devoid of hydrogenase and formic hydrogenlyase but showed formic dehydrogenase activity when adequate amounts of selenium and molybdenum were present in the growth medium. Hydrogenase was consistently absent in iron-deficient cells but appeared concomitantly with formic hydrogenlyase during induced biosynthesis of the latter in iron-deficient cells of E. coli.
J Bacteriol 1965 Sep
PMID:Induced Biosynthesis of Formic Hydrogenlyase in Iron-Deficient Cells of Escherichia coli. 1656 66


<< Previous 1 2 3 4 5 6 7 8 9 10