1WUQ

Structure of GTP cyclohydrolase I Complexed with 8-oxo-GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel reaction mechanism of GTP cyclohydrolase I. High-resolution X-ray crystallography of Thermus thermophilus HB8 enzyme complexed with a transition state analogue, the 8-oxoguanine derivative

Tanaka, Y.Nakagawa, N.Kuramitsu, S.Yokoyama, S.Masui, R.

(2005) J.Biochem.(Tokyo) 138: 263-275

  • DOI: 10.1093/jb/mvi120
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GTP cyclohydrolase I (GTPCH1) catalyzes the conversion of GTP to dihydroneopterin 3'-triphosphate. We found that an 8-oxoguanine derivative of GTP (8-oxo-GTP) strongly bound to GTPCH1 from Thermus thermophilus HB8 (tGTPCH1) as a competitive inhibitor ...

    GTP cyclohydrolase I (GTPCH1) catalyzes the conversion of GTP to dihydroneopterin 3'-triphosphate. We found that an 8-oxoguanine derivative of GTP (8-oxo-GTP) strongly bound to GTPCH1 from Thermus thermophilus HB8 (tGTPCH1) as a competitive inhibitor. The affinity of 8-oxo-GTP was three orders of magnitude greater than that of GTP. These results suggest that 8-oxo-GTP is a transition state analogue of GTPCH1. We have solved the X-ray crystal structures of tGTPCH1 complexed with 8-oxo-GTP and 8-oxo-dGTP at 2.0 and 1.8 A resolution, respectively, as well as the free form of the enzyme at 2.2 A resolution. In the structure of tGTPCH1 complexed with 8-oxo-GTP or 8-oxo-dGTP, the oxygen atoms at O8 of the 8-oxoguanine groups, together with residues Cys108, His111 and Cys179, are coordinated to the zinc ion. The water molecule between Ndelta1 of His177 and N7 of 8-oxoguanine is conserved in both structures. These structural data are in accordance with one of the proposed transition states. Superimpositioning of the structures indicates the imidazole ring of His110 is rotated, implying concomitant proton transfer to the ribose ring O4'. Based on these structural data we propose a novel reaction mechanism for GTPCH1.


    Organizational Affiliation

    Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP cyclohydrolase I
A, B, C, D, E
220Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: folE
EC: 3.5.4.16
Find proteins for Q5SH52 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SH52
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
8GT
Query on 8GT

Download SDF File 
Download CCD File 
A, C, D
8-OXO-GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O15 P3
JCHLKIQZUXYLPW-UMMCILCDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8GTKi: 5.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 160.800α = 90.00
b = 110.957β = 105.53
c = 70.463γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
CNSrefinement
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance