1MEN

complex structure of human GAR Tfase and substrate beta-GAR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structures of human GAR Tfase of low and high pH and with substrate beta-GAR

Zhang, Y., Desharnais, J., Greasley, S.E., Beardsley, G.P., Boger, D.L., Wilson, I.A.

(2002) Biochemistry 41: 14206-14215

  • DOI: 10.1021/bi020522m
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Glycinamide ribonucleotide transformylase (GAR Tfase) is a key folate-dependent enzyme in the de novo purine biosynthesis pathway and, as such, has been the target for antitumor drug design. Here, we describe the crystal structures of the human GAR T ...

    Glycinamide ribonucleotide transformylase (GAR Tfase) is a key folate-dependent enzyme in the de novo purine biosynthesis pathway and, as such, has been the target for antitumor drug design. Here, we describe the crystal structures of the human GAR Tfase (purN) component of the human trifunctional protein (purD-purM-purN) at various pH values and in complex with its substrate. Human GAR Tfase exhibits pH-dependent enzyme activity with its maximum around pH 7.5-8. Comparison of unliganded human GAR Tfase structures at pH 4.2 and pH 8.5 reveals conformational differences in the substrate binding loop, which at pH 4.2 occupies the binding cleft and prohibits substrate binding, while at pH 8.5 is permissive for substrate binding. The crystal structure of GAR Tfase with its natural substrate, beta-glycinamide ribonucleotide (beta-GAR), at pH 8.5 confirms this conformational isomerism. Surprisingly, several important structural differences are found between human GAR Tfase and previously reported E. coli GAR Tfase structures, which have been used as the primary template for drug design studies. While the E. coli structure gave valuable insights into the active site and formyl transfer mechanism, differences in structure and inhibition between the bacterial and mammalian enzymes suggest that the human GAR Tfase structure is now the appropriate template for the design of anti-cancer agents.

    Organizational Affiliation: 

    Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoribosylglycinamide formyltransferase
A, B, C
223Homo sapiensMutation(s): 0 
Gene Names: GART, PGFT, PRGS
EC: 2.1.2.2 (PDB Primary Data), 6.3.4.13 (UniProt), 6.3.3.1 (UniProt)
Find proteins for P22102 (Homo sapiens)
Go to UniProtKB:  P22102
NIH Common Fund Data Resources
PHAROS  P22102
GTEx  ENSG00000159131
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAR
Query on GAR
Download CCD File 
A, B, C
GLYCINAMIDE RIBONUCLEOTIDE
C7 H13 N2 O8 P
OBQMLSFOUZUIOB-SHUUEZRQSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.220 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.825α = 90
b = 147.825β = 90
c = 188.036γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance