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The crystal Structure of the First Enzyme of Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase from Mycobacterium Tuberculosis Shows a Decameric Assembly and Terminal Helix-Swapping

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The Crystal Structure of the First Enzyme in the Pantothenate Biosynthetic Pathway, Ketopantoate Hydroxymethyltransferase, from M. tuberculosis

Chaudhuri, B.N., Sawaya, M.R., Kim, C.Y., Waldo, G.S., Park, M.S., Terwilliger, T.C., Yeates, T.O.

(2003) Structure 11: 753-764


  • PubMed Abstract: 

    • Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate, which is a precursor to coenzyme A and is required for penicillin biosynthesis. The crystal structure of KPHMT from Mycobacterium tu ...

    Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate, which is a precursor to coenzyme A and is required for penicillin biosynthesis. The crystal structure of KPHMT from Mycobacterium tuberculosis was determined by the single anomalous substitution (SAS) method at 2.8 A resolution. KPHMT adopts a structure that is a variation on the (beta/alpha) barrel fold, with a metal binding site proximal to the presumed catalytic site. The protein forms a decameric complex, with subunits in opposing pentameric rings held together by a swapping of their C-terminal alpha helices. The structure reveals KPHMT's membership in a small, recently discovered group of (beta/alpha) barrel enzymes that employ domain swapping to form a variety of oligomeric assemblies. The apparent conservation of certain detailed structural characteristics suggests that KPHMT is distantly related by divergent evolution to enzymes in unrelated pathways, including isocitrate lyase and phosphoenolpyruvate mutase.

    Organizational Affiliation: 

    UCLA Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ketopantoate hydroxymethyltransferase
A, B, C, D, E
281Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: panB
EC: 2.1.2.11
Find proteins for P9WIL7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WIL7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.800α = 90.00
b = 106.800β = 90.00
c = 224.400γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
DMphasing
DMmodel building
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance