5DNA

Crystal structure of Candida boidinii formate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

Guo, Q.Gakhar, L.Wickersham, K.Francis, K.Vardi-Kilshtain, A.Major, D.T.Cheatum, C.M.Kohen, A.

(2016) Biochemistry 55: 2760-2771

  • DOI: 10.1021/acs.biochem.6b00181
  • Primary Citation of Related Structures:  

  • 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 h ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FORMATE DEHYDROGENASE
A, B, C, D
364Candida boidiniiMutation(s): 0 
Gene Names: FDH
EC: 1.17.1.9
Find proteins for A0A0A1EQY0 (Candida boidinii)
Go to UniProtKB:  A0A0A1EQY0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.143 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.711α = 78.11
b = 68.514β = 89.66
c = 109.458γ = 81.24
Software Package:
Software NamePurpose
Cootmodel building
StructureStudiodata collection
SCALAdata scaling
PHENIXrefinement
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references