5DN9

Crystal structure of Candida boidinii formate dehydrogenase complexed with NAD+ and azide

Summary for 5DN9

• Entry DOI: 10.2210/pdb5dn9/pdb
• Related: 5DN4 5DN5 5DNA
• Descriptor: FDH, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, AZIDE ION, ... (5 entities in total)
• Functional Keywords: transition state, ternary complex, oxidoreductase
• Biological source: Candida boidinii (Yeast)
• Total number of polymer chains: 2
• Total formula weight: 82211.73

Authors

Guo, Q.,Gakhar, L.,Wichersham, K.,Francis, K.,Vardi-Kilshtain, A.,Major, D.T.,Cheatum, C.M.,Kohen, A. (deposition date: 2015-09-09, release date: 2016-05-04, Last modification date: 2023-09-27)

Primary citation

Guo, Q.,Gakhar, L.,Wickersham, K.,Francis, K.,Vardi-Kilshtain, A.,Major, D.T.,Cheatum, C.M.,Kohen, A.
Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.
Biochemistry, 55:2760-2771, 2016

PubMed Abstract: The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented.

PubMed: 27100912
DOI: 10.1021/acs.biochem.6b00181

Experimental method

X-RAY DIFFRACTION (1.5 Å)