6PDT

cryoEM structure of yeast glucokinase filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 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
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTRosetta

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary