1YON | pdb_00001yon

Escherichia coli ketopantoate reductase in complex with 2-monophosphoadenosine-5'-diphosphate

• PDB DOI: https://doi.org/10.2210/pdb1YON/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-28 Released: 2006-04-18 
• Deposition Author(s): Ciulli, A., Lobley, C.M.C., Tuck, K.L., Williams, G., Smith, A.G., Blundell, T.L., Abell, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

pH-tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study.

Ciulli, A., Lobley, C.M., Tuck, K.L., Smith, A.G., Blundell, T.L., Abell, C.

(2007) Acta Crystallogr D Biol Crystallogr 63: 171-178

• PubMed: 17242510 
• DOI: https://doi.org/10.1107/S0907444906044465
• Primary Citation Related Structures: 
  1YON


• PubMed Abstract: 
  

  The crystal structure of Escherichia coli ketopantoate reductase in complex with 2'-monophosphoadenosine 5'-diphosphoribose, a fragment of NADP+ that lacks the nicotinamide ring, is reported. The ligand is bound at the enzyme active site in the opposite orientation to that observed for NADP+, with the adenine ring occupying the lipophilic nicotinamide pocket. Isothermal titration calorimetry with R31A and N98A mutants of the enzyme is used to show that the unusual ;reversed binding mode' observed in the crystal is triggered by changes in the protonation of binding groups at low pH. This research has important implications for fragment-based approaches to drug design, namely that the crystallization conditions and the chemical modification of ligands can have unexpected effects on the binding modes.

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Organizational Affiliation: 
• University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, England.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.55 kDa 
• Atom Count: 2,550 
• Modeled Residue Count: 292 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A	303	Escherichia coli	Mutation(s): 0  Gene Names: panE EC: 1.1.1.169
UniProt
Find proteins for P0A9J4 (Escherichia coli (strain K12)) Explore P0A9J4  Go to UniProtKB:  P0A9J4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2R	B [auth A]	[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE C15 H24 N5 O17 P3 ICNHOLCERMYLRZ-KEOHHSTQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.318	α = 90
b = 65.833	β = 90
c = 98.207	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-18 
Deposition Author(s): Ciulli, A., Lobley, C.M.C., Tuck, K.L., Williams, G., Smith, A.G., Blundell, T.L., Abell, C.

Revision History  

• Version 1.0: 2006-04-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-11-19
  Changes: Non-polymer description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary