1RU2

CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E.COLI HPPK(V83G/DEL84-89) WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN AT 1.48 ANGSTROM RESOLUTION (ORTHORHOMBIC FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Essential Roles of a Dynamic Loop in the Catalysis of 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase.

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

(2004) Biochemistry 43: 1469-1477

  • DOI: 10.1021/bi036053l
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphoryl group from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP) following an ordered bi-bi mechanism with ATP as the first substrate. The rate-limiting step ...

    6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphoryl group from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP) following an ordered bi-bi mechanism with ATP as the first substrate. The rate-limiting step of the reaction is product release, and the complete active center is assembled and sealed only upon the binding of both ATP and HP. The assembly of the active center involves large conformational changes in three catalytic loops, among which loop 3 undergoes the most dramatic and unusual changes. To investigate the roles of loop 3 in catalysis, we have made a deletion mutant, which has been investigated by biochemical and X-ray crystallographic analysis. The biochemical data showed that the deletion mutation does not have significant effects on the dissociation constants or the rate constants for the binding of the first substrate MgATP or its analogues. The dissociation constant of HP for the mutant increases by a factor of approximately 100, which is due to a large increase in the dissociation rate constant. The deletion mutation causes a shift of the rate-limiting step in the reaction and a decrease in the rate constant for the chemical step by a factor of approximately 1.1 x 10(5). The crystal structures revealed that the deletion mutation does not affect protein folding, but the catalytic center of the mutant is not fully assembled even upon the formation of the ternary complex and is not properly sealed. The results together suggest that loop 3 is dispensable for the folding of the protein and the binding of the first substrate MgATP, but is required for the assembling and sealing of the active center. The loop plays an important role in the stabilization of the ternary complex and is critical for catalysis.


    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
    • 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
    • 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


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, P.O. Box B, Frederick, Maryland 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
A
152Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: folK
EC: 2.7.6.3
Find proteins for P26281 (Escherichia coli (strain K12))
Go to UniProtKB:  P26281
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HHR
Query on HHR

Download SDF File 
Download CCD File 
A
6-HYDROXYMETHYLPTERIN
C7 H7 N5 O2
XGWIBNWDLMIPNF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
APC
Query on APC

Download SDF File 
Download CCD File 
A
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HHRKd: 18000 nM BINDINGMOAD
APCKd: 320 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.609α = 90.00
b = 63.156β = 90.00
c = 36.201γ = 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: 2003-12-10 
  • Released Date: 2004-02-24 
  • Deposition Author(s): Blaszczyk, J., Ji, X.

Revision History 

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-09-21
    Type: Other