4XYB

GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NADP(+) AND NaN3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for double cofactor specificity in a new formate dehydrogenase from the acidobacterium Granulicella mallensis MP5ACTX8.

Fogal, S.Beneventi, E.Cendron, L.Bergantino, E.

(2015) Appl.Microbiol.Biotechnol. 99: 9541-9554

  • DOI: 10.1007/s00253-015-6695-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Formate dehydrogenases (FDHs) are considered particularly useful enzymes in biocatalysis when the regeneration of the cofactor NAD(P)H is required, that is, in chiral synthesis with dehydrogenases. Their utilization is however limited to the recyclin ...

    Formate dehydrogenases (FDHs) are considered particularly useful enzymes in biocatalysis when the regeneration of the cofactor NAD(P)H is required, that is, in chiral synthesis with dehydrogenases. Their utilization is however limited to the recycling of NAD(+), since all (apart one) of the FDHs characterized so far are strictly specific for this cofactor, and this is a major drawback for their otherwise wide applicability. Despite the many attempts performed to modify cofactor specificity by protein engineering different NAD(+)-dependent FDHs, in the general practice, glucose or phosphite dehydrogenases are chosen for the recycling of NADP(+). We report on the functional and structural characterization of a new FDH, GraFDH, identified by mining the genome of the extremophile prokaryote Granulicella mallensis MP5ACTX8. The new enzyme displays a valuable stability in the presence of many organic cosolvents as well as double cofactor specificity, with NADP(+) preferred over NAD(+) at acidic pH values, at which it also shows the highest stability. The quite low affinities for both cofactors as well as for the substrate formate indicate, however, that the native enzyme requires optimization to be applied as biocatalytic tool. We also determined the crystal structure of GraFDH both as apoprotein and as holoprotein, either in complex with NAD(+) or NADP(+). Noticeably, the latter represents the first structure of an FDH enzyme in complex with NADP(+). This fine picture of the structural determinants involved in cofactor selectivity will possibly boost protein engineering of the new enzyme or other homolog FDHs in view of their biocatalytic exploitation for NADP(+) recycling.


    Organizational Affiliation

    Department of Biology, University of Padova, Viale G.Colombo 3, 35121, Padova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formate dehydrogenase
A, B
391Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8)Mutation(s): 0 
EC: 1.17.1.9
Find proteins for G8NVB5 (Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8))
Go to UniProtKB:  G8NVB5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
A, B
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.056α = 90.00
b = 113.804β = 90.00
c = 116.191γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references