1BWF

ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.168 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Crystal structures of Escherichia coli glycerol kinase variant S58-->W in complex with nonhydrolyzable ATP analogues reveal a putative active conformation of the enzyme as a result of domain motion.

Bystrom, C.E.Pettigrew, D.W.Branchaud, B.P.O'Brien, P.Remington, S.J.

(1999) Biochemistry 38: 3508-3518

  • DOI: https://doi.org/10.1021/bi982460z
  • Primary Citation of Related Structures:  
    1BWF, 1GLJ, 1GLL

  • PubMed Abstract: 

    Escherichia coli glycerol kinase (GK) displays "half-of-the-sites" reactivity toward ATP and allosteric regulation by fructose 1, 6-bisphosphate (FBP), which has been shown to promote dimer-tetramer assembly and to inhibit only tetramers. To probe the role of tetramer assembly, a mutation (Ser58-->Trp) was designed to sterically block formation of the dimer-dimer interface near the FBP binding site [Ormo, M., Bystrom, C., and Remington, S. J. (1998) Biochemistry 37, 16565-16572]. The substitution did not substantially change the Michaelis constants or alter allosteric regulation of GK by a second effector, the phosphocarrier protein IIAGlc; however, it eliminated FBP inhibition. Crystal structures of GK in complex with different nontransferable ATP analogues and glycerol revealed an asymmetric dimer with one subunit adopting an open conformation and the other adopting the closed conformation found in previously determined structures. The conformational difference is produced by a approximately 6.0 degrees rigid-body rotation of the N-terminal domain with respect to the C-terminal domain, similar to that observed for hexokinase and actin, members of the same ATPase superfamily. Two of the ATP analogues bound in nonproductive conformations in both subunits. However, beta, gamma-difluoromethyleneadenosine 5'-triphosphate (AMP-PCF2P), a potent inhibitor of GK, bound nonproductively in the closed subunit and in a putative productive conformation in the open subunit, with the gamma-phosphate placed for in-line transfer to glycerol. This asymmetry is consistent with "half-of-the-sites" reactivity and suggests that the inhibition of GK by FBP is due to restriction of domain motion.


  • Organizational Affiliation

    Institute of Molecular Biology, Departments of Physics and Chemistry, University of Oregon, Eugene, Oregon 97403, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCEROL KINASEA [auth Y],
B [auth O]
501Escherichia coliMutation(s): 1 
EC: 2.7.1.30
UniProt
Find proteins for P0A6F3 (Escherichia coli (strain K12))
Explore P0A6F3 
Go to UniProtKB:  P0A6F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6F3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.767α = 90
b = 200.293β = 90
c = 114.738γ = 90
Software Package:
Software NamePurpose
TNTrefinement
SDMSdata reduction
SDMSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2023-08-09
    Changes: Refinement description
  • Version 1.5: 2024-05-22
    Changes: Data collection