BRENDA - Enzyme Database
show all sequences of 1.2.5.3

The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase

Hanzelmann, P.; Dobbek, H.; Gremer, L.; Huber, R.; Meyer, O.; J. Mol. Biol. 301, 1221-1235 (2000)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
crystallization at high (Moplus CODH)cand low intracellular molybdenum content (Mominus CODH), hanging drop vapour-diffusion method, Moplus CODH species at 2.5 units/mg obtained by mixing 0.006 ml of protein in 50 mM Hepes/NaOH, pH 7.2, with 0.002 ml of reservoir solution containing 1.1 M NaK-tartrate, 0.3 M (NH4)H2PO4, pH 7.2, 3% w/v methylpentanediol, and 10 mM dithioerythritol, 1-2 weeks, 4°C, from the Mominus CODH species (0.02 units/mg) under the same crystallization conditions only strong bunched crystals in a brown precipitate emerge. Crystals suitable for X-ray data collection are prepared by repeated washing of these crystals with crystallizing agent to remove precipitate, redissolving of crystals in 50 mM Hepes/NaOH followed by recrystallization under the above conditions, X-ray diffraction structure determination and analysis at 2.25 A and 2.35 A resolution, respectively
Hydrogenophaga pseudoflava
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
in type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
Mo
the pentacoordinated Mo(VI) exhibits a distorted square pyramidal coordination geometry. Function of the Mo ion in the proper orientation of active-site residues S-selanyl-Cys385 and Glu757. Mo is an absolute requirement for the conversion of molybdopterin to MCD, a tricyclic tetra-hydropterin-pyran system reduced by two electrons when compared to the fully oxidized state, as well as for the insertion of the Mocofactor into CODH
Hydrogenophaga pseudoflava
additional information
the structure of the catalytically inactive Mominus CODH indicates that an intracellular Mo-deficiency affects exclusively the active site of the enzyme as an incomplete non-functional molybdenum cofactor is synthesized. The 5'-CDP residue is present in Mominus CODH, whereas the Mo-pyranopterin moiety is absent. In Moplus CODH the selenium faces the Mo ion and flips away from the Mo site in Mominus CODH
Hydrogenophaga pseudoflava
Se
active-site residues S-selanyl-Cys385 and Glu757
Hydrogenophaga pseudoflava
[2Fe-2S] cluster
type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
CO + a quinone + H2O
Hydrogenophaga pseudoflava
-
CO2 + a quinol
-
-
?
CO + a quinone + H2O
Hydrogenophaga pseudoflava DSM 1084
-
CO2 + a quinol
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Hydrogenophaga pseudoflava
P19915
formerly Pseudomonas carboxydoflava
-
Hydrogenophaga pseudoflava DSM 1084
P19915
formerly Pseudomonas carboxydoflava
-
Posttranslational Modification
Posttranslational Modification
Commentary
Organism
additional information
enzyme from Hydrogenophaga pseudoflava reveals a unique posttranslationally modified Cg-hydroxy-Arg384 residue which precedes the catalytically essential S-selanyl-Cys385 in the active-site loop
Hydrogenophaga pseudoflava
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava
CO2 + a quinol
-
-
-
?
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava DSM 1084
CO2 + a quinol
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
active site and cofactor binding structure, overview
Hydrogenophaga pseudoflava
Cofactor
Cofactor
Commentary
Organism
Structure
FAD
FAD is bound in a fold formed by the N-terminal and middle domains. In the N-terminal domain a beta-turn part of a betaalphabeta-unit of a three-stranded parallel beta-sheet contains the motif 32AGGHS36 which interacts with the FAD diphosphate. FAD binding structure, overview
Hydrogenophaga pseudoflava
additional information
a seleno-molybdo-iron-sulfur-flavoprotein
Hydrogenophaga pseudoflava
seleno-molybdenum-cofactor
analysis of the architecture and arrangements of the molybdopterin-cytosine dinucleotide-type of the molybdenum cofactor. The hydrogen bonding interaction pattern of the molybdenum cofactor involves 27 hydrogen bonds with the surrounding protein. Of these, eight are with the cytosine moiety, eight with the diphosphate, six with the pyranopterin, and five with the ligands of the Mo. A 5'-CDP residue is present in Mominus CODH, whereas the Mo-pyranopterin moiety is absent. Different side-chain conformations of the active site residues S-selanyl-Cys385 and Glu757 in Moplus and Mominus CODH indicate a side-chain flexibility and a function of the Mo ion in the proper orientation of both residues. Function of the Mo ion in the proper orientation of active-site residues S-selanyl-Cys385 and Glu757. Mo is an absolute requirement for the conversion of molybdopterin to MCD, a tricyclic tetra-hydropterin-pyran system reduced by two electrons when compared to the fully oxidized state, as well as for insertion of the Mo cofactor into CODH
Hydrogenophaga pseudoflava
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
FAD
FAD is bound in a fold formed by the N-terminal and middle domains. In the N-terminal domain a beta-turn part of a betaalphabeta-unit of a three-stranded parallel beta-sheet contains the motif 32AGGHS36 which interacts with the FAD diphosphate. FAD binding structure, overview
Hydrogenophaga pseudoflava
additional information
a seleno-molybdo-iron-sulfur-flavoprotein
Hydrogenophaga pseudoflava
seleno-molybdenum-cofactor
analysis of the architecture and arrangements of the molybdopterin-cytosine dinucleotide-type of the molybdenum cofactor. The hydrogen bonding interaction pattern of the molybdenum cofactor involves 27 hydrogen bonds with the surrounding protein. Of these, eight are with the cytosine moiety, eight with the diphosphate, six with the pyranopterin, and five with the ligands of the Mo. A 5'-CDP residue is present in Mominus CODH, whereas the Mo-pyranopterin moiety is absent. Different side-chain conformations of the active site residues S-selanyl-Cys385 and Glu757 in Moplus and Mominus CODH indicate a side-chain flexibility and a function of the Mo ion in the proper orientation of both residues. Function of the Mo ion in the proper orientation of active-site residues S-selanyl-Cys385 and Glu757. Mo is an absolute requirement for the conversion of molybdopterin to MCD, a tricyclic tetra-hydropterin-pyran system reduced by two electrons when compared to the fully oxidized state, as well as for insertion of the Mo cofactor into CODH
Hydrogenophaga pseudoflava
Crystallization (Commentary) (protein specific)
Crystallization
Organism
crystallization at high (Moplus CODH)cand low intracellular molybdenum content (Mominus CODH), hanging drop vapour-diffusion method, Moplus CODH species at 2.5 units/mg obtained by mixing 0.006 ml of protein in 50 mM Hepes/NaOH, pH 7.2, with 0.002 ml of reservoir solution containing 1.1 M NaK-tartrate, 0.3 M (NH4)H2PO4, pH 7.2, 3% w/v methylpentanediol, and 10 mM dithioerythritol, 1-2 weeks, 4°C, from the Mominus CODH species (0.02 units/mg) under the same crystallization conditions only strong bunched crystals in a brown precipitate emerge. Crystals suitable for X-ray data collection are prepared by repeated washing of these crystals with crystallizing agent to remove precipitate, redissolving of crystals in 50 mM Hepes/NaOH followed by recrystallization under the above conditions, X-ray diffraction structure determination and analysis at 2.25 A and 2.35 A resolution, respectively
Hydrogenophaga pseudoflava
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
in type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
Mo
the pentacoordinated Mo(VI) exhibits a distorted square pyramidal coordination geometry. Function of the Mo ion in the proper orientation of active-site residues S-selanyl-Cys385 and Glu757. Mo is an absolute requirement for the conversion of molybdopterin to MCD, a tricyclic tetra-hydropterin-pyran system reduced by two electrons when compared to the fully oxidized state, as well as for the insertion of the Mocofactor into CODH
Hydrogenophaga pseudoflava
additional information
the structure of the catalytically inactive Mominus CODH indicates that an intracellular Mo-deficiency affects exclusively the active site of the enzyme as an incomplete non-functional molybdenum cofactor is synthesized. The 5'-CDP residue is present in Mominus CODH, whereas the Mo-pyranopterin moiety is absent. In Moplus CODH the selenium faces the Mo ion and flips away from the Mo site in Mominus CODH
Hydrogenophaga pseudoflava
Se
active-site residues S-selanyl-Cys385 and Glu757
Hydrogenophaga pseudoflava
[2Fe-2S] cluster
type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
CO + a quinone + H2O
Hydrogenophaga pseudoflava
-
CO2 + a quinol
-
-
?
CO + a quinone + H2O
Hydrogenophaga pseudoflava DSM 1084
-
CO2 + a quinol
-
-
?
Posttranslational Modification (protein specific)
Posttranslational Modification
Commentary
Organism
additional information
enzyme from Hydrogenophaga pseudoflava reveals a unique posttranslationally modified Cg-hydroxy-Arg384 residue which precedes the catalytically essential S-selanyl-Cys385 in the active-site loop
Hydrogenophaga pseudoflava
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava
CO2 + a quinol
-
-
-
?
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava DSM 1084
CO2 + a quinol
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
active site and cofactor binding structure, overview
Hydrogenophaga pseudoflava
General Information
General Information
Commentary
Organism
additional information
structure analysis and architecture of enzyme synthesized at high (Moplus CODH) and low intracellular molybdenum content (Mominus CODH), both sources are structurally very much conserved and show the same overall fold, architecture and arrangements of the molybdopterin-cytosine-dinucleotide-type of molybdenum cofactor, the type I and type II [2Fe-2S] clusters and the flavinadenine dinucleotide. The different side-chain conformations of the active-site residues S-selanyl-Cys385 and Glu757 in Moplus and Mominus CODH indicate a side-chain flexibility and a function of the Mo ion in the proper orientation of both residues. The structure of the catalytically inactive Mominus CODH indicates that an intracellular Mo-deficiency affects exclusively the active site of the enzyme as an incomplete non-functional molybdenum cofactor is synthesized. The 5'-CDP residue is present in Mominus CODH, whereas the Mo-pyranopterin moiety is absent. In Moplus CODH the selenium faces the Mo ion and flips away from the Mo site in Mominus CODH. Active site structure, overview
Hydrogenophaga pseudoflava
General Information (protein specific)
General Information
Commentary
Organism
additional information
structure analysis and architecture of enzyme synthesized at high (Moplus CODH) and low intracellular molybdenum content (Mominus CODH), both sources are structurally very much conserved and show the same overall fold, architecture and arrangements of the molybdopterin-cytosine-dinucleotide-type of molybdenum cofactor, the type I and type II [2Fe-2S] clusters and the flavinadenine dinucleotide. The different side-chain conformations of the active-site residues S-selanyl-Cys385 and Glu757 in Moplus and Mominus CODH indicate a side-chain flexibility and a function of the Mo ion in the proper orientation of both residues. The structure of the catalytically inactive Mominus CODH indicates that an intracellular Mo-deficiency affects exclusively the active site of the enzyme as an incomplete non-functional molybdenum cofactor is synthesized. The 5'-CDP residue is present in Mominus CODH, whereas the Mo-pyranopterin moiety is absent. In Moplus CODH the selenium faces the Mo ion and flips away from the Mo site in Mominus CODH. Active site structure, overview
Hydrogenophaga pseudoflava
Other publictions for EC 1.2.5.3
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
736514
Hille
The aerobic CO dehydrogenase f ...
Oligotropha carboxidovorans
J. Biol. Inorg. Chem.
20
243-251
2015
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4
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735935
Stein
Orbital contributions to CO ox ...
Hydrogenophaga pseudoflava, Oligotropha carboxidovorans
Chem. Commun. (Camb.)
50
1104-1106
2014
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4
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736513
Pelzmann
Insights into the posttranslat ...
Oligotropha carboxidovorans
J. Biol. Inorg. Chem.
19
1399-1414
2014
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4
4
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736437
Wilcoxen
The hydrogenase activity of th ...
Oligotropha carboxidovorans
J. Biol. Chem.
288
36052-36060
2013
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1
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725197
Wilcoxen
Substitution of silver for cop ...
Oligotropha carboxidovorans
J. Am. Chem. Soc.
133
12934-12936
2011
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1
1
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3
3
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735667
Wilcoxen
Reaction of the molybdenum- an ...
, Oligotropha carboxidovorans ATCC 49405
Biochemistry
50
1910-1916
2011
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2
2
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725052
Nishimura
-
Purification and characterizat ...
Aeropyrum pernix, Aeropyrum pernix TB5
Fish. Sci.
76
999-1006
2010
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1
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4
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2
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725392
Zhang
Kinetic and spectroscopic stud ...
Oligotropha carboxidovorans
J. Biol. Chem.
285
12571-12578
2010
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736301
Gourlay
Paramagnetic active site model ...
Oligotropha carboxidovorans
J. Am. Chem. Soc.
128
2164-2165
2006
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736512
Resch
Structural and functional reco ...
Oligotropha carboxidovorans, Oligotropha carboxidovorans DSM 1227
J. Biol. Inorg. Chem.
10
518-528
2005
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390484
Lorite
Carbon monoxide dehydrogenase ...
Bradyrhizobium japonicum, Bradyrhizobium japonicum 110spc4
Appl. Environ. Microbiol.
66
1871-1876
2000
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656481
Hanzelmann
The effect of intracellular mo ...
Hydrogenophaga pseudoflava, Hydrogenophaga pseudoflava DSM 1084
J. Mol. Biol.
301
1221-1235
2000
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1
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736397
Gremer
Binding of flavin adenine dinu ...
Oligotropha carboxidovorans, Oligotropha carboxidovorans DSM 1227
J. Biol. Chem.
275
1864-1872
2000
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4
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2
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390482
Dobbek
Crystal structure and mechanis ...
Oligotropha carboxidovorans
Proc. Natl. Acad. Sci. USA
96
8884-8889
1999
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1
1
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3
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3
1
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4
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1
1
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1
1
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390483
Kang
Cloning and molecular characte ...
Hydrogenophaga pseudoflava, Hydrogenophaga pseudoflava DSM 1084
J. Bacteriol.
181
5581-5590
1999
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3
3
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2
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1
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1
1
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3
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1
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2
1
1
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1
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3
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1
1
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390479
Schubel
Molecular characterization of ...
Oligotropha carboxidovorans, Oligotropha carboxidovorans OM5
J. Bacteriol.
177
2197-2203
1995
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