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 
  • R-Value Observed: 0.160 

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:  
    3IP0, 1HQ2, 1IM6, 1KBR, 1F9H, 1G4C

  • 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 conserved in 35 HPPK sequences, play dynamic roles in the catalytic cycle of the enzyme ...

    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: 
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASEA158Escherichia coliMutation(s): 1 
EC: 2.7.6.3
UniProt
Find proteins for P26281 (Escherichia coli (strain K12))
Explore P26281 
Go to UniProtKB:  P26281
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth 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 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.34α = 90
b = 46.943β = 110.49
c = 42.907γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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