1KBR

CRYSTAL STRUCTURE OF UNLIGATED HPPK(R92A) FROM E.COLI AT 1.55 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dynamic Roles of Arginine Residues 82 and 92 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase: Crystallographic Studies

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

(2003) Biochemistry 42: 1573-1580

  • DOI: 10.1021/bi0267994
  • Primary Citation of Related Structures:  1F9H, 1F9Y, 1G4C, 1HQ2, 1IM6, 3H4A, 3IP0

  • PubMed Abstract: 
  • 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate biosynthetic pathway. Arginine residues 82 and 92, strictly conserve ...

    6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate biosynthetic pathway. Arginine residues 82 and 92, strictly conserved in 35 HPPK sequences, play dynamic roles in the catalytic cycle of the enzyme. At 0.89-A resolution, two distinct conformations are observed for each of the two residues in the crystal structure of the wild-type HPPK in complex with two HP variants, two Mg(2+) ions, and an ATP analogue. Structural information suggests that R92 first binds to the alpha-phosphate group of ATP and then shifts to interact with the beta-phosphate as R82, which initially does not bind to ATP, moves in and binds to alpha-phosphate when the pyrophosphoryl transfer is about to occur. The dynamic roles of R82 and R92 are further elucidated by five more crystal structures of two mutant proteins, R82A and R92A, with and without bound ligands. Two oxidized forms of HP are observed with an occupancy ratio of 0.50:0.50 in the 0.89-A structure. The oxidation of HP has significant impact on its binding to the protein as well as the conformation of nearby residue W89.


    Related Citations: 
    • Unusual Conformational Changes in 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase Revealed by X-Ray Crystallography and NMR
      Xiao, B.,Shi, G.,Gao, J.,Blaszczyk, J.,Liu, Q.,Ji, X.,Yan, H.
      (2001) J.Biol.Chem. 276: 40274
    • 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
    • Bisubstrate Analogue Inhibitors of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase: Synthesis and Biochemical and Crystallographic Studies
      Shi, G.,Blaszczyk, J.,Ji, X.,Yan, H.
      (2001) J.Med.Chem. 44: 1364
    • 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, Maryland 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-HYDROXYMETHYL-7,8-DIHYDROPTERIN 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
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.340α = 90.00
b = 46.943β = 110.49
c = 42.907γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-11-06 
  • Released Date: 2003-04-15 
  • Deposition Author(s): Blaszczyk, J., Ji, X.

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance