1EQM

CRYSTAL STRUCTURE OF BINARY COMPLEX OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE WITH ADENOSINE-5'-DIPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as 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: 40274-40281

  • DOI: 10.1074/jbc.M103837200
  • Primary Citation of Related Structures:  
  • Also Cited By: 3HT0, 3HD2, 3HD1

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in complex with MgADP has been determined at 1.5-A resolution with a crystallographic R factor of 0.191. The solution structure of HPPK in complex wi ...

    The crystal structure of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) in complex with MgADP has been determined at 1.5-A resolution with a crystallographic R factor of 0.191. The solution structure of HPPK in complex with Mg(2+) and beta,gamma-methyleneadenosine 5'-triphosphate (MgAMPPCP) has been determined using a simulated annealing protocol with 3,523 experimental NMR restraints. The root mean square deviation of the ensemble of 20 refined conformers that represent the solution structure from the mean coordinate set derived from them is 0.74 +/- 0.26 A for all backbone atoms and 0.49 +/- 0.22 A when residues Pro(14), Pro(44)-Gln(50), and Arg(84)-Pro(91) are excluded. Binding of MgADP causes significant changes in the conformation and dynamical property of three loops of HPPK that are involved in catalysis. A dramatic, unusual conformational change is that loop 3 moves away from the active center significantly with some residues moving by >17 A. The binding of MgADP also stabilizes loop 1 and loop 3 but makes loop 2 more mobile. Very similar conformational and dynamical changes are observed in the NMR solution structure of HPPK.MgAMPPCP. The conformational and dynamical changes may play important roles in both substrate binding and product release in the catalytic cycle.


    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


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, NCI, National Institutes of Health, Frederick, MD 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)Mutation(s): 0 
Gene Names: folK
EC: 2.7.6.3
Find proteins for P26281 (Escherichia coli (strain K12))
Go to UniProtKB:  P26281
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.140α = 90.00
b = 52.800β = 103.43
c = 36.640γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
SHELXL-97refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance