4JKI

Crystal Strucutre of N10-Formyltetrahydrofolate Synthetase with ZD9331, Formylphosphate, and ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of N10-formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors.

Celeste, L.R.Chai, G.Bielak, M.Minor, W.Lovelace, L.L.Lebioda, L.

(2012) Protein Sci. 21: 219-228

  • DOI: 10.1002/pro.2005
  • Primary Citation of Related Structures:  
  • Also Cited By: 4IOM, 4IOL, 4IOK, 4IOJ

  • PubMed Abstract: 
  • N(10) -formyltetrahydrofolate synthetase (FTHFS) is a folate enzyme that catalyzes the formylation of tetrahydrofolate (THF) in an ATP dependent manner. Structures of FTHFS from the thermophilic homoacetogen, Moorella thermoacetica, complexed with (1 ...

    N(10) -formyltetrahydrofolate synthetase (FTHFS) is a folate enzyme that catalyzes the formylation of tetrahydrofolate (THF) in an ATP dependent manner. Structures of FTHFS from the thermophilic homoacetogen, Moorella thermoacetica, complexed with (1) a catalytic intermediate-formylphosphate (XPO) and product-ADP; (2) with an inhibitory substrate analog-folate; (3) with XPO and an inhibitory THF analog, ZD9331, were used to analyze the enzyme mechanism. Nucleophilic attack of the formate ion on the gamma phosphate of ATP leads to the formation of XPO and the first product ADP. A channel that leads to the putative formate binding pocket allows for the binding of ATP and formate in random order. Formate binding is due to interactions with the gamma-phosphate moiety of ATP and additionally to two hydrogen bonds from the backbone nitrogen of Ala276 and the side chain of Arg97. Upon ADP dissociation, XPO reorients and moves to the position previously occupied by the beta-phosphate of ATP. Conformational changes that occur due to the XPO presence apparently allow for the recruitment of the third substrate, THF, with its pterin moiety positioned between Phe384 and Trp412. This position overlaps with that of the bound nucleoside, which is consistent with a catalytic mechanism hypothesis that FTHFS works via a sequential ping-pong mechanism. More specifically, a random bi uni uni bi ping-pong ter ter mechanism is proposed. Additionally, the native structure originally reported at a 2.5 Å resolution was redetermined at a 2.2 Å resolution.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter St., Columbia, SC 29208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formate--tetrahydrofolate ligase
A, B
559Moorella thermoacetica (strain ATCC 39073 / JCM 9320)Mutation(s): 0 
Gene Names: fhs
EC: 6.3.4.3
Find proteins for Q2RM91 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Go to UniProtKB:  Q2RM91
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZD9
Query on ZD9

Download SDF File 
Download CCD File 
A
2,7-dimethyl-6-[(prop-1-yn-1-ylamino)methyl]quinazolin-4(3H)-one
C14 H15 N3 O
VHJQNTIPWBTKDM-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
XPO
Query on XPO

Download SDF File 
Download CCD File 
A
formyl phosphate
C H3 O5 P
TVISEJUYYBUVNV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.186 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 162.373α = 90.00
b = 162.373β = 90.00
c = 258.074γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description