1M3U

Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of E. coli Ketopantoate Hydroxymethyl Transferase Complexed with Ketopantoate and Mg(2+), Solved by Locating 160 Selenomethionine Sites.

von Delft, F.Inoue, T.Saldanha, S.A.Ottenhof, H.H.Schmitzberger, F.Birch, L.M.Dhanaraj, V.Witty, M.Smith, A.G.Blundell, T.L.Abell, C.

(2003) Structure 11: 985-996


  • PubMed Abstract: 
  • We report the crystal structure of E. coli ketopantoate hydroxymethyltransferase (KPHMT) at 1.9 A resolution, in complex with its product, ketopantoate. KPHMT catalyzes the first step in the biosynthesis of pantothenate (vitamin B(5)), the precursor ...

    We report the crystal structure of E. coli ketopantoate hydroxymethyltransferase (KPHMT) at 1.9 A resolution, in complex with its product, ketopantoate. KPHMT catalyzes the first step in the biosynthesis of pantothenate (vitamin B(5)), the precursor of coenzyme A and the acyl carrier protein cofactor. The structure of the decameric enzyme was solved by multiwavelength anomalous dispersion to locate 160 selenomethionine sites and phase 560 kDa of protein, making it the largest structure solved by this approach. KPHMT adopts the (betaalpha)(8) barrel fold and is a member of the phosphoenolpyruvate/pyruvate superfamily. The active site contains a ketopantoate bidentately coordinated to Mg(2+). Similar binding is likely for the substrate, alpha-ketoisovalerate, orienting the C3 for deprotonation.


    Related Citations: 
    • Ketopantoate Hydroxymethyltransferase. II. Physical, Catalytic, and Regulatory Properties.
      Powers, S.G.,Snell, E.E.
      (1976) J.Biol.Chem. 251: 3786
    • Ketopantoate Hydroxymethyltransferase. I. Purification and Role in Pantothenate Biosynthesis.
      Teller, J.H.,Powers, S.G.,Snell, E.E.
      (1976) J.Biol.Chem. 251: 3780
    • Cloning and Sequencing of the Escherichia coli panB gene, which encodes ketopantoate hydroxymethyltransferase, and overexpression of the enzyme.
      Jones, C.E.,Brook, J.M.,Buck, D.,Abell, C.,Smith, A.G.
      (1993) J.BACTERIOL. 175: 2125


    Organizational Affiliation

    Department of Biochemistry, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-methyl-2-oxobutanoate hydroxymethyltransferase
A, B, C, D, E, F, G, H, I, J
264Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: panB
EC: 2.1.2.11
Find proteins for P31057 (Escherichia coli (strain K12))
Go to UniProtKB:  P31057
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KPL
Query on KPL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
KETOPANTOATE
2-DEHYDROPANTOATE
C6 H10 O4
PKVVTUWHANFMQC-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.074α = 90.00
b = 157.170β = 97.44
c = 100.181γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
SnBphasing
CCP4data scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description