5LRB

Plastidial phosphorylase from Barley in complex with acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Functional and structural characterization of plastidic starch phosphorylase during barley endosperm development.

Cuesta-Seijo, J.A.Ruzanski, C.Krucewicz, K.Meier, S.Hagglund, P.Svensson, B.Palcic, M.M.

(2017) PLoS ONE 12: e0175488-e0175488

  • DOI: 10.1371/journal.pone.0175488
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The production of starch is essential for human nutrition and represents a major metabolic flux in the biosphere. The biosynthesis of starch in storage organs like barley endosperm operates via two main pathways using different substrates: starch syn ...

    The production of starch is essential for human nutrition and represents a major metabolic flux in the biosphere. The biosynthesis of starch in storage organs like barley endosperm operates via two main pathways using different substrates: starch synthases use ADP-glucose to produce amylose and amylopectin, the two major components of starch, whereas starch phosphorylase (Pho1) uses glucose-1-phosphate (G1P), a precursor for ADP-glucose production, to produce α-1,4 glucans. The significance of the Pho1 pathway in starch biosynthesis has remained unclear. To elucidate the importance of barley Pho1 (HvPho1) for starch biosynthesis in barley endosperm, we analyzed HvPho1 protein production and enzyme activity levels throughout barley endosperm development and characterized structure-function relationships of HvPho1. The molecular mechanisms underlying the initiation of starch granule biosynthesis, that is, the enzymes and substrates involved in the initial transition from simple sugars to polysaccharides, remain unclear. We found that HvPho1 is present as an active protein at the onset of barley endosperm development. Notably, purified recombinant protein can catalyze the de novo production of α-1,4-glucans using HvPho1 from G1P as the sole substrate. The structural properties of HvPho1 provide insights into the low affinity of HvPho1 for large polysaccharides like starch or amylopectin. Our results suggest that HvPho1 may play a role during the initiation of starch biosynthesis in barley.


    Organizational Affiliation

    Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-1,4 glucan phosphorylase
A, B
938Hordeum vulgare subsp. vulgareMutation(s): 0 
EC: 2.4.1.1
Find proteins for F2E0G2 (Hordeum vulgare subsp. vulgare)
Go to UniProtKB:  F2E0G2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
ACR
Query on ACR

Download SDF File 
Download CCD File 
A, B
ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX-5,6-ENYL)AMINO)FRUCTOSE
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 230.330α = 90.00
b = 63.680β = 115.07
c = 149.330γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release