8R4G

Plastidial phosphorylase Pho1 from Solanum tuberosum in complex with a-D-glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Kinetic and Structural Studies of the Plastidial Solanum tuberosum Phosphorylase.

Koulas, S.M.Kyriakis, E.Tsagkarakou, A.S.Leonidas, D.D.

(2024) ACS Omega 9: 41841-41854

  • DOI: https://doi.org/10.1021/acsomega.4c06313
  • Primary Citation of Related Structures:  
    8R48, 8R49, 8R4G, 8R4J, 8R4K

  • PubMed Abstract: 

    Kinetics and structural studies of the plastidial Solanum tuberosum phosphorylase ( st Pho1) revealed that the most active form of the enzyme ( st Pho1ΔL78) is composed by two segments generated by proteolytic degradation of an approximately 65-residue-long peptide (L78) approximately in the middle of the st Pho1 primary structure. st Pho1ΔL78 is 1.5 times more active than the nonproteolyzed enzyme in solution and shows stronger specificity for glycogen, α-d-glucose, caffeine, and β-cyclodextrin than st Pho1. The crystal structure of st Pho1ΔL78 has been resolved at 2.2 Å resolution and revealed similarities and differences with the mammalian enzymes. The structural fold is conserved as is the active site, while other binding sites such as the inhibitor, the glycogen storage, the quercetin, and the allosteric are not. The binding of α-d-glucose, caffeine, and β-cyclodextrin to st Pho1 has been studied by X-ray crystallography and revealed significant differences from those of the mammalian phosphorylases. As st Pho1 is capable of catalyzing both starch synthesis and degradation, our studies suggest that the direction of st Pho1 activity is regulated by the proteolytic degradation of the L78 peptide.


  • Organizational Affiliation

    Department of Biochemistry & Biotechnology, University of Thessaly, Biopolis 41500, Larissa, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1,4 glucan phosphorylase L-1 isozyme, chloroplastic/amyloplastic
A, B, C
916Solanum tuberosumMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P04045 (Solanum tuberosum)
Explore P04045 
Go to UniProtKB:  P04045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04045
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLC (Subject of Investigation/LOI)
Query on GLC

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.233α = 90
b = 125.913β = 90.05
c = 117.075γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references