2IV2

Reinterpretation of reduced form of formate dehydrogenase H from E. coli

Summary for 2IV2

• Entry DOI: 10.2210/pdb2iv2/pdb
• Related: 1AA6 1FDI 1FDO
• Descriptor: Formate dehydrogenase H, IRON/SULFUR CLUSTER, GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER, ... (7 entities in total)
• Functional Keywords: oxidoreductase, 4fe-4s, naerobic, dehydrogenase, fe4s4, formate, iron, iron sulfur cluster, iron-sulfur, metal-binding, mgd, molybdenum, molybdopterin, molybdopterin guanine dinucleotide, mpt, nad, secys, selenium, selenocysteine
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 81396.41

Authors

Raaijmakers, H.C.A.,Romao, M.J. (deposition date: 2006-06-08, release date: 2006-06-12, Last modification date: 2023-12-13)

Primary citation

Raaijmakers, H.C.A.,Romao, M.J.
Formate-Reduced E. Coli Formate Dehydrogenase H: The Reinterpretation of the Crystal Structure Suggests a New Reaction Mechanism.
J.Biol.Inorg.Chem., 11:849-, 2006

PubMed Abstract: Re-evaluation of the crystallographic data of the molybdenum-containing E. coli formate dehydrogenase H (Boyington et al. Science 275:1305-1308, 1997), reported in two redox states, reveals important structural differences for the formate-reduced form, with large implications for the reaction mechanism proposed in that work. We have re-refined the reduced structure with revised protocols and found substantial rearrangement in some parts of it. The original model is essentially correct but an important loop close to the molybdenum active site was mistraced, and, therefore, catalytic relevant residues were located in wrong positions. In particular selenocysteine-140, a ligand of molybdenum in the original work, and essential for catalysis, is no longer bound to the metal after reduction of the enzyme with formate. These results are incompatible with the originally proposed reaction mechanism. On the basis of our new interpretation, we have revised and proposed a new reaction mechanism, which reconciles the new X-ray model with previous biochemical and extended X-ray absorption fine structure data.

PubMed: 16830149
DOI: 10.1007/S00775-006-0129-2

Experimental method

X-RAY DIFFRACTION (2.27 Å)