3FN4

Apo-form of NAD-dependent formate dehydrogenase from bacterium Moraxella sp.C-1 in closed conformation

Summary for 3FN4

• Entry DOI: 10.2210/pdb3fn4/pdb
• Related: 2FSS 2GSD 2NAC 2NAD
• Descriptor: NAD-dependent formate dehydrogenase, GLYCEROL, SULFATE ION, ... (4 entities in total)
• Functional Keywords: homodimer, closed conformation of apo-form, oxidoreductase
• Biological source: Moraxella sp.
• Cellular location: Cytoplasm : O08375
• Total number of polymer chains: 1
• Total formula weight: 44255.79

Authors

Shabalin, I.G.,Polyakov, K.M.,Filippova, E.V.,Dorovatovskiy, P.V.,Tikhonova, T.V.,Sadykhov, E.G.,Tishkov, V.I.,Popov, V.O. (deposition date: 2008-12-23, release date: 2009-12-01, Last modification date: 2023-09-06)

Primary citation

Shabalin, I.G.,Filippova, E.V.,Polyakov, K.M.,Sadykhov, E.G.,Safonova, T.N.,Tikhonova, T.V.,Tishkov, V.I.,Popov, V.O.
Structures of the apo and holo forms of formate dehydrogenase from the bacterium Moraxella sp. C-1: towards understanding the mechanism of the closure of the interdomain cleft
Acta Crystallogr.,Sect.D, 65:1315-1325, 2009

PubMed Abstract: NAD(+)-dependent formate dehydrogenase (FDH) catalyzes the oxidation of formate ion to carbon dioxide coupled with the reduction of NAD(+) to NADH. The crystal structures of the apo and holo forms of FDH from the methylotrophic bacterium Moraxella sp. C-1 (MorFDH) are reported at 1.96 and 1.95 A resolution, respectively. MorFDH is similar to the previously studied FDH from the bacterium Pseudomonas sp. 101 in overall structure, cofactor-binding mode and active-site architecture, but differs in that the eight-residue-longer C-terminal fragment is visible in the electron-density maps of MorFDH. MorFDH also differs in the organization of the dimer interface. The holo MorFDH structure supports the earlier hypothesis that the catalytic residue His332 can form a hydrogen bond to both the substrate and the transition state. Apo MorFDH has a closed conformation of the interdomain cleft, which is unique for an apo form of an NAD(+)-dependent dehydrogenase. A comparison of the structures of bacterial FDH in open and closed conformations allows the differentiation of the conformational changes associated with cofactor binding and domain motion and provides insights into the mechanism of the closure of the interdomain cleft in FDH. The C-terminal residues 374-399 and the substrate (formate ion) or inhibitor (azide ion) binding are shown to play an essential role in the transition from the open to the closed conformation.

PubMed: 19966418
DOI: 10.1107/S0907444909040773

Experimental method

X-RAY DIFFRACTION (1.96 Å)