5DN9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
FDH
A, B
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
A, B
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.931α = 90.00
b = 116.617β = 106.90
c = 63.208γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
Cootmodel building
XDSdata scaling
REFMACrefinement
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM065368
National Science Foundation (United States)United StatesCHE-1149023
United States - Israel Binational Science FoundationIsrael2012340
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079368

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description