1FZT

SOLUTION STRUCTURE AND DYNAMICS OF AN OPEN B-SHEET, GLYCOLYTIC ENZYME-MONOMERIC 23.7 KDA PHOSPHOGLYCERATE MUTASE FROM SCHIZOSACCHAROMYCES POMBE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 55 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Solution structure and dynamics of an open beta-sheet, glycolytic enzyme, monomeric 23.7 kDa phosphoglycerate mutase from Schizosaccharomyces pombe.

Uhrinova, S.Uhrin, D.Nairn, J.Price, N.C.Fothergill-Gilmore, L.A.Barlow, P.N.

(2001) J Mol Biol 306: 275-290

  • DOI: https://doi.org/10.1006/jmbi.2000.4390
  • Primary Citation of Related Structures:  
    1FZT

  • PubMed Abstract: 

    The structure and backbone dynamics of a double labelled (15N,13C) monomeric, 23.7 kD phosphoglycerate mutase (PGAM) from Schizosaccharomyces pombe have been investigated in solution using NMR spectroscopy. A set of 3125 NOE-derived distance restraints, 148 restraints representing inferred hydrogen bonds and 149 values of (3)J(HNHalpha) were used in the structure calculation. The mean rmsd from the average structure for all backbone atoms from residues 6-205 in the best 21 calculated structures was 0.59 A. The core of the enzyme includes an open, twisted, six-stranded beta-sheet flanked by four alpha-helices and a short 3(10)-helix. An additional smaller domain contains two short antiparallel beta-strands and a further pair of alpha-helices. The C(alpha) atoms of the S. pombe PGAM may be superimposed on their equivalents in one of the four identical subunits of Saccharomyces cerevisiae PGAM with an rmsd of 1.34 A (0.92 A if only the beta-sheet is considered). Small differences between the two structures are attributable partly to the deletion in the S. pombe sequence of a 25 residue loop involved in stabilising the S. cerevisiae tetramer. Analysis of 15N relaxation parameters indicates that PGAM tumbles isotropically with a rotational correlation time of 8.7 ns and displays a range of dynamic features. Of 178 residues analysed, only 77 could be fitted without invoking terms for fast internal motion or chemical exchange, and out of the remainder, 77 required a chemical exchange term. Significantly, 46 of the slowly exchanging (milli- to microsecond) residues lie in helices, and these account for two-thirds of all analysed helix residues. On the contrary, only one beta-sheet residue required an exchange term. In contrast to other analyses of backbone dynamics reported previously, residues in slow exchange appeared to correlate with architectural features of the enzyme rather than congregating close to ligand binding sites.


  • Organizational Affiliation

    Edinburgh Centre for Protein Technology, University of Edinburgh, Joseph Black Building, West Mains Road, Edinburgh, EH9 3JJ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOGLYCERATE MUTASE211Schizosaccharomyces pombeMutation(s): 0 
EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
UniProt
Find proteins for P36623 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P36623 
Go to UniProtKB:  P36623
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36623
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 55 
  • Conformers Submitted: 21 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-14
    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: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection