BRENDA - Enzyme Database

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)
EC Number
Crystallization
Organism
1.2.5.3
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
Localization
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
1.2.2.4
Mo6+
functions in the proper orientation of the catalytically active residues C385 and E757, crystalization data
Hydrogenophaga pseudoflava
1.2.5.3
Fe2+
in type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
1.2.5.3
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
1.2.5.3
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
1.2.5.3
Se
active-site residues S-selanyl-Cys385 and Glu757
Hydrogenophaga pseudoflava
1.2.5.3
[2Fe-2S] cluster
type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.2.5.3
CO + a quinone + H2O
Hydrogenophaga pseudoflava
-
CO2 + a quinol
-
-
?
1.2.5.3
CO + a quinone + H2O
Hydrogenophaga pseudoflava DSM 1084
-
CO2 + a quinol
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.2.2.4
Hydrogenophaga pseudoflava
P19913
carbon monoxide dehydrogenase large chain
-
1.2.5.3
Hydrogenophaga pseudoflava
P19915
formerly Pseudomonas carboxydoflava
-
1.2.5.3
Hydrogenophaga pseudoflava DSM 1084
P19915
formerly Pseudomonas carboxydoflava
-
Posttranslational Modification
EC Number
Posttranslational Modification
Commentary
Organism
1.2.2.4
molybdoironflavoprotein
-
Hydrogenophaga pseudoflava
1.2.2.4
additional information
R384 has a gamma-hydroxy modification, C385 carries the catalytically essential S-selanyl-group
Hydrogenophaga pseudoflava
1.2.5.3
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)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.2.5.3
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava
CO2 + a quinol
-
-
-
?
1.2.5.3
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava DSM 1084
CO2 + a quinol
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.2.5.3
More
active site and cofactor binding structure, overview
Hydrogenophaga pseudoflava
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.2.5.3
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
1.2.5.3
additional information
a seleno-molybdo-iron-sulfur-flavoprotein
Hydrogenophaga pseudoflava
1.2.5.3
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)
EC Number
Cofactor
Commentary
Organism
Structure
1.2.5.3
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
1.2.5.3
additional information
a seleno-molybdo-iron-sulfur-flavoprotein
Hydrogenophaga pseudoflava
1.2.5.3
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)
EC Number
Crystallization
Organism
1.2.5.3
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
Localization (protein specific)
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
1.2.2.4
Mo6+
functions in the proper orientation of the catalytically active residues C385 and E757, crystalization data
Hydrogenophaga pseudoflava
1.2.5.3
Fe2+
in type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
1.2.5.3
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
1.2.5.3
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
1.2.5.3
Se
active-site residues S-selanyl-Cys385 and Glu757
Hydrogenophaga pseudoflava
1.2.5.3
[2Fe-2S] cluster
type I and type II [2Fe-2S] clusters
Hydrogenophaga pseudoflava
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.2.5.3
CO + a quinone + H2O
Hydrogenophaga pseudoflava
-
CO2 + a quinol
-
-
?
1.2.5.3
CO + a quinone + H2O
Hydrogenophaga pseudoflava DSM 1084
-
CO2 + a quinol
-
-
?
Posttranslational Modification (protein specific)
EC Number
Posttranslational Modification
Commentary
Organism
1.2.2.4
molybdoironflavoprotein
-
Hydrogenophaga pseudoflava
1.2.2.4
additional information
R384 has a gamma-hydroxy modification, C385 carries the catalytically essential S-selanyl-group
Hydrogenophaga pseudoflava
1.2.5.3
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)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.2.5.3
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava
CO2 + a quinol
-
-
-
?
1.2.5.3
CO + a quinone + H2O
-
656481
Hydrogenophaga pseudoflava DSM 1084
CO2 + a quinol
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.2.5.3
More
active site and cofactor binding structure, overview
Hydrogenophaga pseudoflava
General Information
EC Number
General Information
Commentary
Organism
1.2.5.3
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)
EC Number
General Information
Commentary
Organism
1.2.5.3
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