1XUP | pdb_00001xup

ENTEROCOCCUS CASSELIFLAVUS GLYCEROL KINASE COMPLEXED WITH GLYCEROL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.268 (Depositor) 
  • R-Value Work: 
    0.242 (Depositor) 
  • R-Value Observed: 
    0.242 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structures of Enterococcal Glycerol Kinase in the Absence and Presence of Glycerol: Correlation of Conformation to Substrate Binding and a Mechanism of Activation by Phosphorylation

Yeh, J.I.Charrier, V.Paulo, J.Hou, L.Darbon, E.Clairborn, A.Hol, W.G.J.Deutscher, J.

(2004) Biochemistry 43: 362-367

  • DOI: https://doi.org/10.1021/bi034258o
  • Primary Citation Related Structures: 
    1R59, 1XUP

  • PubMed Abstract: 

    The first structure of a glycerol kinase from a Gram-positive organism, Enterococcus casseliflavus, has been determined to 2.8 A resolution in the presence of glycerol and to 2.5 A resolution in the absence of substrate. The substrate-induced closure of 7 degrees is significantly smaller than that reported for hexokinase, a model for substrate-mediated domain closure that has been proposed for glycerol kinase. Despite the 78% level of sequence identity and conformational similarity in the catalytic cleft regions of the En. casseliflavus and Escherichia coli glycerol kinases, remarkable structural differences have now been identified. These differences correlate well with their divergent regulatory schemes of activation by phosphorylation in En. casseliflavus and allosteric inhibition in E. coli. On the basis of our structural results, we propose a mechanism by which the phosphorylation of a histidyl residue located 25 A from the active site results in a 10-15-fold increase in the activity of the enterococcal glycerol kinase.


  • Organizational Affiliation
    • Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA. Joanne_Yeh@brown.edu

Macromolecule Content 

  • Total Structure Weight: 107.46 kDa 
  • Atom Count: 7,557 
  • Modeled Residue Count: 974 
  • Deposited Residue Count: 974 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycerol kinaseA [auth O],
B [auth X]
487Enterococcus casseliflavusMutation(s): 0 
Gene Names: glpK
EC: 2.7.1.30
UniProt
Find proteins for O34153 (Enterococcus casseliflavus)
Explore O34153 
Go to UniProtKB:  O34153
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34153
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.268 (Depositor) 
  • R-Value Work:  0.242 (Depositor) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.01α = 90
b = 107.67β = 90
c = 201.45γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations