4TS4

Crystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (wild-type) from zebrafish


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition.

Lin, C.C.Chuankhayan, P.Chang, W.N.Kao, T.T.Guan, H.H.Fun, H.K.Nakagawa, A.Fu, T.F.Chen, C.J.

(2015) Acta Crystallogr.,Sect.D 71: 1006-1021

  • DOI: 10.1107/S1399004715002928
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 10-Formyltetrahydrofolate dehydrogenase (FDH), which is composed of a small N-terminal domain (Nt-FDH) and a large C-terminal domain, is an abundant folate enzyme in the liver and converts 10-formyltetrahydrofolate (10-FTHF) to tetrahydrofolate (THF) ...

    10-Formyltetrahydrofolate dehydrogenase (FDH), which is composed of a small N-terminal domain (Nt-FDH) and a large C-terminal domain, is an abundant folate enzyme in the liver and converts 10-formyltetrahydrofolate (10-FTHF) to tetrahydrofolate (THF) and CO2. Nt-FDH alone possesses a hydrolase activity, which converts 10-FTHF to THF and formate in the presence of β-mercaptoethanol. To elucidate the catalytic mechanism of Nt-FDH, crystal structures of apo-form zNt-FDH from zebrafish and its complexes with the substrate analogue 10-formyl-5,8-dideazafolate (10-FDDF) and with the products THF and formate have been determined. The structures reveal that the conformations of three loops (residues 86-90, 135-143 and 200-203) are altered upon ligand (10-FDDF or THF) binding in the active site. The orientations and geometries of key residues, including Phe89, His106, Arg114, Asp142 and Tyr200, are adjusted for substrate binding and product release during catalysis. Among them, Tyr200 is especially crucial for product release. An additional potential THF binding site is identified in the cavity between two zNt-FDH molecules, which might contribute to the properties of product inhibition and THF storage reported for FDH. Together with mutagenesis studies and activity assays, the structures of zNt-FDH and its complexes provide a coherent picture of the active site and a potential THF binding site of zNt-FDH along with the substrate and product specificity, lending new insights into the molecular mechanism underlying the enzymatic properties of Nt-FDH.


    Organizational Affiliation

    Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan.,Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan City 701, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
10-formyltetrahydrofolate dehydrogenase
A
318Danio rerioMutation(s): 0 
Gene Names: aldh1l1
EC: 1.5.1.6
Find proteins for E3NZ06 (Danio rerio)
Go to UniProtKB:  E3NZ06
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.665α = 90.00
b = 53.878β = 90.00
c = 60.632γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Council (NSC)Taiwan98-2313-B-009-001-MY3
National Science Council (NSC)Taiwan101-2628-B-213-001-MY4
National Science Council (NSC)Taiwan102-2627-M-213-001-MY3
National Synchrotron Radiation Center (NSRRC)Taiwan1013RSB02
National Synchrotron Radiation Center (NSRRC)Taiwan1023RSB02
National Science Council (NSC)Taiwan99-2320-B-006-013-MY3
Deanship of Scientific Research at King Saud UniversitySaudi ArabiaRGP-VPP-207

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 2.0: 2019-12-18
    Type: Atomic model, Data collection, Database references, Derived calculations, Other, Source and taxonomy