Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.51 kDa 
• Atom Count: 3089 
• Modelled Residue Count: 318 
• Deposited Residue Count: 318 
• Unique protein chains: 1

2QX0

Crystal Structure of Yersinia pestis HPPK (Ternary Complex)

• PDB DOI: 10.2210/pdb2QX0/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-10 Released: 2007-10-23 
• Deposition Author(s): Blaszczyk, J., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

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

• PubMed: 18007032 
• DOI: 10.1107/S0907444907047452
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase	A, B	159	Yersinia pestis	Mutation(s): 0  Gene Names: folK, YPO3400, G4D65_01490, G4D67_03070, GD372_03530 EC: 2.7.6.3
UniProt
Find proteins for A0A5P8YCA3 (Yersinia pestis) Explore A0A5P8YCA3  Go to UniProtKB:  A0A5P8YCA3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APC	E [auth A], I [auth B]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H18 N5 O12 P3 CAWZRIXWFRFUQB-IOSLPCCCSA-N
PH2	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	C [auth A], D [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
PH2	PDBBind:  2QX0	Kd: 780 (nM) from 1 assay(s)
	Binding MOAD:  2QX0	Kd: 780 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.4	α = 90
b = 78.62	β = 100.72
c = 52.6	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-10 
• Released Date: 2007-10-23 
Deposition Author(s): Blaszczyk, J., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance