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Literature summary extracted from

  • Hanzelmann, P.; Dobbek, H.; Gremer, L.; Huber, R.; Meyer, O.
    The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase (2000), J. Mol. Biol., 301, 1221-1235.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) 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 Comment Organism GeneOntology No. Textmining

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
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 Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 UniProt Comment Textmining
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 Comment Organism
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 Comment Substrates Organism Products Comment (Products) Rev. Reac.
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
-
 ?

Subunits

EC Number Subunits Comment Organism
1.2.5.3 More active site and cofactor binding structure, overview Hydrogenophaga pseudoflava

Synonyms

EC Number Synonyms Comment Organism
1.2.5.3 Carbon monoxide dehydrogenase
-
 Hydrogenophaga pseudoflava
1.2.5.3 CODH
-
 Hydrogenophaga pseudoflava

Cofactor

EC Number Cofactor Comment 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

General Information

EC Number General Information Comment 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