6P4X

Crystal Structure of the S. cerevisiae glucokinase, Glk1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.269 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Polymerization in the actin ATPase clan regulates hexokinase activity in yeast.

Stoddard, P.R.Lynch, E.M.Farrell, D.P.Dosey, A.M.DiMaio, F.Williams, T.A.Kollman, J.M.Murray, A.W.Garner, E.C.

(2020) Science 367: 1039-1042

  • DOI: https://doi.org/10.1126/science.aay5359
  • Primary Citation of Related Structures:  
    6P4X, 6PDT

  • PubMed Abstract: 

    The actin fold is found in cytoskeletal polymers, chaperones, and various metabolic enzymes. Many actin-fold proteins, such as the carbohydrate kinases, do not polymerize. We found that Glk1, a Saccharomyces cerevisiae glucokinase, forms two-stranded filaments with ultrastructure that is distinct from that of cytoskeletal polymers. In cells, Glk1 polymerized upon sugar addition and depolymerized upon sugar withdrawal. Polymerization inhibits enzymatic activity; the Glk1 monomer-polymer equilibrium sets a maximum rate of glucose phosphorylation regardless of Glk1 concentration. A mutation that eliminated Glk1 polymerization alleviated concentration-dependent enzyme inhibition. Yeast containing nonpolymerizing Glk1 were less fit when growing on sugars and more likely to die when refed glucose. Glk1 polymerization arose independently from other actin-related filaments and may allow yeast to rapidly modulate glucokinase activity as nutrient availability changes.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucokinase-1
A, B, C, D, E
A, B, C, D, E, F
500Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GLK1HOR3YCL040WYCL312YCL40W
EC: 2.7.1.2
UniProt
Find proteins for P17709 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17709 
Go to UniProtKB:  P17709
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17709
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth E],
Q [auth E],
R [auth F],
S [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.267 
  • R-Value Observed: 0.269 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.75α = 90
b = 177.75β = 90
c = 323.947γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF31GM116441
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2AI117923

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2020-04-22
    Changes: Derived calculations
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description