Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content

• Total Structure Weight: 284.35 kDa 
• Atom Count: 22849 
• Modelled Residue Count: 2620 
• Deposited Residue Count: 2640 
• Unique protein chains: 1

1M3U

Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate

• DOI: 10.2210/pdb1M3U/pdb

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


• Deposited: 2002-06-30 Released: 2003-07-22 
• Deposition Author(s): von Delft, F., Inoue, T., Saldanha, S.A., Ottenhof, H.H., Dhanaraj, V., Witty, M., Abell, C., Smith, A.G., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

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: 12906829 
• DOI: 10.1016/s0969-2126(03)00158-8
• Primary Citation of Related Structures:  
  1M3U


• 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 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.

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Related Citations: 

• Ketopantoate Hydroxymethyltransferase. I. Purification and Role in Pantothenate Biosynthesis.
  Teller, J.H., Powers, S.G., Snell, E.E.
  (1976) J Biol Chem 251: 3780

• Ketopantoate Hydroxymethyltransferase. II. Physical, Catalytic, and Regulatory Properties.
  Powers, S.G., Snell, E.E.
  (1976) J Biol Chem 251: 3786

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methyl-2-oxobutanoate hydroxymethyltransferase	A, B, C, D, E, F, G, H, I, J	264	Escherichia coli	Mutation(s): 0  Gene Names: panB EC: 2.1.2.11
Find proteins for P31057 (Escherichia coli (strain K12)) Explore P31057  Go to UniProtKB:  P31057

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KPL	BA [auth I],  DA [auth J],  L [auth A],  N [auth B],  P [auth C],  R [auth D],  T [auth E],  V [auth F],  X [auth G],  Z [auth H]	KETOPANTOATE C6 H10 O4 PKVVTUWHANFMQC-UHFFFAOYSA-N
MG	AA [auth I],  CA [auth J],  K [auth A],  M [auth B],  O [auth C],  Q [auth D],  S [auth E],  U [auth F],  W [auth G],  Y [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.193 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.074	α = 90
b = 157.17	β = 97.44
c = 100.181	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SnB	phasing
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-30 
• Released Date: 2003-07-22 
Deposition Author(s): von Delft, F., Inoue, T., Saldanha, S.A., Ottenhof, H.H., Dhanaraj, V., Witty, M., Abell, C., Smith, A.G., Blundell, T.L.

Revision History  

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