Hydrogenase enzymes
Hydrogenases
Anaerobic bacteria:
-production of H2 during fermentation of sugars
-the use of H2 in the reduction of CO2 to methane or other
compounds.
-parallel hydogenase function of nitrogenase enzymes
-H2 as biological energy source
1. Iron hydrogenases
1. Iron hydrogenases
1. Iron hydrogenases
F cluster - Fe4S4+/2+ type, and ESR signal characteristic to the S=1/2
spin state in the reduced state of the enzyme.
H cluster – hydrogen activation site; its oxidised form is ESR active.
1. Iron hydrogenases
Both H2 oxidation and production of H2
22Fe: 4F, 1H
H2-oxidation
14Fe: 2F (F,F’), 1H
The redox potential of the F/S clusters of the C. Pasteurianum
bacterium at pH ~ 8, and the mechanism of the hydrogenase II:
1. Iron hydrogenases
The H cluster
X-ray structure of the hydrogenase I enzyme of the C. Pasteurianum
bacterium
[Peters, J. W., Lanzilotta, W. N., Lemon, B. J. & Seefeldt, L. C. (1998) Science,
282, 1853–1858.]
1. Iron hydrogenases
eI
0
I
Fe
Fe
Fe
H+
I
Fe
Cys
0
-
e
H2
H2
-
+
H
Fe
Fe
OC
CN
S
CO
4Fe4S
-
e
CN
CO
-
e
e
H
+
H
H
H
+
H
S
S
H
II
Fe
I
Fe
Cys
H
II
Fe
II
I
Fe
S
S
Fe
Fe
OC
CN
S
CO
4Fe4S
-
e
CN
CO
H+
Schematic pictures of the hydrogen production and oxidation (A), and
the direction of the electron transfer during reduction of the proton and
oxidation of the H2 (B).
2. Nickel-iron hydrogenases
+H2
Schematic drawing of the mechanism of the hydrogenase enzyme
2. Nickel-iron hydrogenases
X-ray structure of the NiFe hidrogenase enzyme of D. Gigas bacterium.
On the right side the active centre of the enzyme is depicted, X = Fe, L1–
3 = CN– and CO ligands, positions I and II indicate the H2 binding sites.
Bioinorganic chemistry of the C1 compounds
Bioinorganic chemistry of
the C1 compounds
Main steps of reduction of CO2 to methane, and the necessary cofactors. Binding
sites of the C1 compounds are indicated by arrows in the formula of the cofactors.
1. Methyl coenzyme M reductase
Assumed mechanism of the methyl-coenzyme M reductase enzyme
1. Methyl coenzyme M reductase
Structure of F430 coenzyme
COO
O
-
H
HN
CH3
H3C
H2NOC
N
COO-
N
Ni+
H
-
OOC
N
N
COO-
H
O
COO-
1. Methyl coenzyme M reductase
The role of nickel in the reaction:
1. Binding of the substrate thioether or thiol groups.
2. Cleavage of the C–S bond (see Raney-Ni as desulfurilation
catalyst).
3. Short life methyl binding site.
4. Oxidativ link of the sulfur atoms to disulfid.
2. CO-dehydrogenase = CO-oxidoreductase
= Acethyl-CoA-synthase
CO-dehydrogenase
Acethyl-CoA-synthase
2. CO-dehydrogenase = CO-oxidoreductase
= Acethyl-CoA-synthase
Mechanism of the acethyl coenzyme A-synthase enzyme
2. CO-dehydrogenase = CO-oxidoreductase
= Acethyl-CoA-synthase
A
B
X-ray structure of the acethyl-coenzyme A synthase enzyme of the C.
hydrogenoformans (A) and the schematic picture of the active centre
with several bond lengths
Other redoxienzymes in biological processes
1. Transformation of nucleotides: ribonucleotide
reductase enzymes
1. Transformation of nucleotides: ribonucleotide reductase
1. Transformation of nucleotides: ribonucleotide reductase
A
B
X-ray structure of the active centre of class I (A) and III (B) bacterial RR
enzymes
1. Transformation of nucleotides: ribonucleotide reductase
The dinuclear iron centre of ribonucleotide reductase enzyme of E. Coli
2. Methane monooxygenase
Schematic mechanism of the sMMO enzyme
3. Oxotransferase enzymes
Schematic structure of the molybdopterine cofactor
3. Oxotransferase enzymes
Probable mechanism of the sulfite-oxidase enzyme
4. Alcohol-dehydrogenase enzymes
4. Alcohol-dehydrogenase enzymes
Structure and NADH binding site of the ADH enzyme of Pseudomonas aeruginosa
4. Alcohol-dehydrogenase enzymes
Active centre (the substrate analogue ethyleneglycole is bound to the
zinc(II) ion) of the ADH enzyme of Pseudomonas aeruginosa . Protein
Science (2004), 13:1547–1556.