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Catalytic Site Atlas

CSA LITERATURE entry for 1kqf

E.C. nameformate dehydrogenase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 1.2.1.2
CSA Homologues of 1kqf
CSA Entries With UniProtID P24183
CSA Entries With EC Number 1.2.1.2
PDBe Entry 1kqf
PDBSum Entry 1kqf
MACiE Entry 1kqf

Literature Report

IntroductionFormate dehydrogenase-N (Fdn-N) isolated from Escherichia coli catalyses the oxidation of formate to carbon dioxide and a proton, coupled to the reduction of menaquinone to menaquinol. Fdn-N is involved in nitrate respiration and forms a redox loop with dissimilatory nitrate reductase (Nar). Together they pump protons across the membrane by reducing menaquinone at Fdn-N (taking up protons from the cytoplasm) and oxidising menaquinol at Nar, (releasing protons into the periplasm). They also generate a membrane potential by moving electrons from Fdn-N to Nar.
Fdn-N contains an active site for formate oxidation (alpha subunit) and an active site for menaquinone reduction (gamma subunit). They are linked by a redox chain containing two haem groups (gamma), five [4Fe-4S] clusters (FeS-0 in alpha and FeS-1 to FeS-4 in beta) and a molybdenum(VI) ion coordinated to two molybdopterin-guanine dinucleotides, the selenate group from Se-Cys196(alpha) and a hydroxide ion (alpha).
MechansimFormate displaces the selenate group of Se-Cys196(alpha) from the Mo(VI) centre. His197(alpha) accepts a proton from formate, which leads to the formation of carbon dioxide (possibly via a selenium-carboxylated intermediate) and the reduction of the molybdenum centre to Mo(IV). The selenate group then re-coordinates to the metal centre. An electron is passed down a chain of iron-sulfur centres in the order FeS-0, FeS-1, FeS-4, FeS-2 and then FeS-3. It is transferred to haem bp, haem bc and then His169(gamma). Menaquinone accepts the electron from His169(gamma) and a proton through a water chain to form menasemiquinone. Mo(V) donates another electron and menasemiquinone is reduced to menaquinol and accepts a proton from His169(gamma). Menaquinol is released and His169(gamma) is protonated through a water channel.
Reaction

Catalytic Sites for 1kqf

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA197197macie:sideChainHis197(alpha) accepts a proton during the two-electron oxidation of formate.
CseA196196macie:sideChainThe selenate group of Se-Cys196(alpha) is displaced from the molybdenum centre by formate. It is thought to be involved in a selenium-carboxylated intermediate before carbon dioxide is released. Once this has occurred the selenate can re-coordinate to the molybdenum centre.
HisC169169macie:sideChainHis169(gamma) is a ligand for haem bc. It transfers electrons from the haem group to menaquinone/menasemiquinone. It also donates a proton to O-1 upon the reduction of menasemiquinone. It is reprotonated only after the menaquinol has been released and a water chain has formed.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA197197macie:sideChainHis197(alpha) accepts a proton during the two-electron oxidation of formate.
CseA196196macie:sideChainThe selenate group of Se-Cys196(alpha) is displaced from the molybdenum centre by formate. It is thought to be involved in a selenium-carboxylated intermediate before carbon dioxide is released. Once this has occurred the selenate can re-coordinate to the molybdenum centre.
HisC169169macie:sideChainHis169(gamma) is a ligand for haem bc. It transfers electrons from the haem group to menaquinone/menasemiquinone. It also donates a proton to O-1 upon the reduction of menasemiquinone. It is reprotonated only after the menaquinol has been released and a water chain has formed.

Literature References

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