1IHO

CRYSTAL APO-STRUCTURE OF PANTOTHENATE SYNTHETASE FROM E. COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

The crystal structure of E. coli pantothenate synthetase confirms it as a member of the cytidylyltransferase superfamily.

von Delft, F.Lewendon, A.Dhanaraj, V.Blundell, T.L.Abell, C.Smith, A.G.

(2001) Structure 9: 439-450

  • DOI: https://doi.org/10.1016/s0969-2126(01)00604-9
  • Primary Citation of Related Structures:  
    1IHO

  • PubMed Abstract: 

    Pantothenate synthetase (EC 6.3.2.1) is the last enzyme of the pathway of pantothenate (vitamin B(5)) synthesis. It catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction. We describe the overexpression, purification, and crystal structure of recombinant pantothenate synthetase from E. coli. The structure was solved by a selenomethionine multiwavelength anomalous dispersion experiment and refined against native data to a final R(cryst) of 22.6% (R(free) = 24.9%) at 1.7 A resolution. The enzyme is dimeric, with two well-defined domains per protomer: the N-terminal domain, a Rossmann fold, contains the active site cavity, with the C-terminal domain forming a hinged lid. The N-terminal domain is structurally very similar to class I aminoacyl-tRNA synthetases and is thus a member of the cytidylyltransferase superfamily. This relationship has been used to suggest the location of the ATP and pantoate binding sites and the nature of hinge bending that leads to the ternary enzyme-pantoate-ATP complex.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PANTOATE--BETA-ALANINE LIGASE
A, B
283Escherichia coliMutation(s): 0 
Gene Names: panc
EC: 6.3.2.1
UniProt
Find proteins for P31663 (Escherichia coli (strain K12))
Explore P31663 
Go to UniProtKB:  P31663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31663
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.031α = 90
b = 78.075β = 103.71
c = 77.126γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SHARPphasing
REFMACrefinement
ARPmodel building
BUSTERrefinement
TNTrefinement
SHELXmodel building
Omodel building
SnBphasing
MOSFLMdata reduction
CCP4data scaling
BUSTERphasing
TNTphasing
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.7: 2024-04-03
    Changes: Refinement description