1RB0

CRYSTAL STRUCTURE OF A BINARY COMPLEX OF E. COLI HPPK WITH 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE AT 1.35 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.

Blaszczyk, J.Shi, G.Li, Y.Yan, H.Ji, X.

(2004) Structure 12: 467-475

  • DOI: 10.1016/j.str.2004.02.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the Mg(2+)-dependent pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The reaction follows a bi-bi mechanism with ATP as the first substrate and AMP and H ...

    6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the Mg(2+)-dependent pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The reaction follows a bi-bi mechanism with ATP as the first substrate and AMP and HP pyrophosphate (HPPP) as the two products. HPPK is a key enzyme in the folate biosynthetic pathway and is essential for microorganisms but absent from mammals. For the HPPK-catalyzed pyrophosphoryl transfer, a reaction coordinate is constructed on the basis of the thermodynamic and transient kinetic data we reported previously, and the reaction trajectory is mapped out with five three-dimensional structures of the enzyme at various liganded states. The five structures are apo-HPPK (ligand-free enzyme), HPPK.MgATP(analog) (binary complex of HPPK with its first substrate) and HPPK.MgATP(analog).HP (ternary complex of HPPK with both substrates), which we reported previously, and HPPK.AMP.HPPP (ternary complex of HPPK with both product molecules) and HPPK.HPPP (binary complex of HPPK with one product), which we present in this study.


    Related Citations: 
    • Catalytic Center Assembly of Hppk as Revealed by the Crystal Structure of a Ternary Complex at 1.25 A Resolution
      Blaszczyk, J.,Shi, G.,Yan, H.,Ji, X.
      (2000) Structure 8: 1049
    • Crystal Structure of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase, a Potential Target for the Development of Novel Antimicrobial Agents
      Xiao, B.,Shi, G.,Chen, X.,Yan, H.,Ji, X.
      (1999) Structure 7: 489


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
A
158Escherichia coli (strain K12)Gene Names: folK
EC: 2.7.6.3
Find proteins for P26281 (Escherichia coli (strain K12))
Go to UniProtKB:  P26281
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HH2
Query on HH2

Download SDF File 
Download CCD File 
A
6-HYDROXYMETHYLPTERIN-DIPHOSPHATE
[PTERIN-6-YL METHANYL]-PHOSPHONOPHOSPHATE
C7 H9 N5 O8 P2
AMDUVUKDRBIVAH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.137 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.591α = 90.00
b = 67.519β = 90.00
c = 35.165γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-10-31 
  • Released Date: 2004-11-09 
  • Deposition Author(s): Blaszczyk, J., Ji, X.

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance