2QX0 | pdb_00002qx0

Crystal Structure of Yersinia pestis HPPK (Ternary Complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.269 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeutics.

Blaszczyk, J.Li, Y.Cherry, S.Alexandratos, J.Wu, Y.Shaw, G.Tropea, J.E.Waugh, D.S.Yan, H.Ji, X.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1169-1177

  • DOI: https://doi.org/10.1107/S0907444907047452
  • Primary Citation Related Structures: 
    2QX0

  • PubMed Abstract: 

    6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a key enzyme in the folate-biosynthetic pathway and is essential for microorganisms but absent from mammals. HPPK catalyzes Mg(2+)-dependent pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). Previously, three-dimensional structures of Escherichia coli HPPK (EcHPPK) have been determined at almost every stage of its catalytic cycle and the reaction mechanism has been established. Here, the crystal structure of Yersinia pestis HPPK (YpHPPK) in complex with HP and an ATP analog is presented together with thermodynamic and kinetic characterizations. The two HPPK molecules differ significantly in a helix-loop area (alpha2-Lp3). YpHPPK has lower affinities than EcHPPK for both nucleotides and HP, but its rate constants for the mechanistic steps of both chemical transformation and product release are comparable with those of EcHPPK. Y. pestis, which causes plague, is a category A select agent according to the Centers for Disease Control and Prevention (CDC). Therefore, these structural and biochemical data are valuable for the design of novel medical countermeasures against plague.


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

Macromolecule Content 

  • Total Structure Weight: 37.51 kDa 
  • Atom Count: 3,089 
  • Modeled Residue Count: 318 
  • Deposited Residue Count: 318 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase
A, B
159Yersinia pestisMutation(s): 0 
Gene Names: folK
EC: 2.7.6.3
UniProt
Find proteins for A0A5P8YCA3 (Yersinia pestis)
Explore A0A5P8YCA3 
Go to UniProtKB:  A0A5P8YCA3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P8YCA3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC

Query on APC



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
PH2

Query on PH2



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE
C7 H9 N5 O2
CQQNNQTXUGLUEV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.269 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.4α = 90
b = 78.62β = 100.72
c = 52.6γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-11-06
    Changes: Structure summary