4F7V | pdb_00004f7v

Crystal structure of E. coli HPPK in complex with bisubstrate analogue inhibitor J1D (HP26)

• PDB DOI: https://doi.org/10.2210/pdb4F7V/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-16 Released: 2012-07-11 
• Deposition Author(s): Shaw, G., Shi, G., Ji, X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Bisubstrate analog inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New lead exhibits a distinct binding mode.

Shi, G., Shaw, G., Li, Y., Wu, Y., Yan, H., Ji, X.

(2012) Bioorg Med Chem 20: 4303-4309

• PubMed: 22727779 
• DOI: https://doi.org/10.1016/j.bmc.2012.05.060
• Primary Citation Related Structures: 
  4F7V


• PubMed Abstract: 
  

  6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), a key enzyme in the folate biosynthesis pathway catalyzing the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin, is an attractive target for developing novel antimicrobial agents. Previously, we studied the mechanism of HPPK action, synthesized bisubstrate analog inhibitors by linking 6-hydroxymethylpterin to adenosine through phosphate groups, and developed a new generation of bisubstrate inhibitors by replacing the phosphate bridge with a piperidine-containing linkage. To further improve linker properties, we have synthesized a new compound, characterized its protein binding/inhibiting properties, and determined its structure in complex with HPPK. Surprisingly, this inhibitor exhibits a new binding mode in that the adenine base is flipped when compared to previously reported structures. Furthermore, the side chain of amino acid residue E77 is involved in protein-inhibitor interaction, forming hydrogen bonds with both 2' and 3' hydroxyl groups of the ribose moiety. Residue E77 is conserved among HPPK sequences, but interacts only indirectly with the bound MgATP via water molecules. Never observed before, the E77-ribose interaction is compatible only with the new inhibitor-binding mode. Therefore, this compound represents a new direction for further development.

---

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 18.6 kDa 
• Atom Count: 1,505 
• Modeled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	A	158	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0142, foIK, folK, JW0138 EC: 2.7.6.3
UniProt
Find proteins for P26281 (Escherichia coli (strain K12)) Explore P26281  Go to UniProtKB:  P26281

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J1D	B [auth A]	5'-{[2-({N-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]glycyl}amino)ethyl]sulfonyl}-5'-deoxyadenosine C23 H30 N12 O8 S QCWCABDSXQYDST-GWKRVTOESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
J1D	BindingDB:  4F7V	Kd: 4160 (nM) from 1 assay(s)
		IC50: 9530 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.118	α = 90
b = 70.581	β = 90
c = 36.261	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Shaw, G., Shi, G., Ji, X.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Refinement description