6GNE

Catalytic domain of Starch Synthase IV from Arabidopsis thaliana bound to ADP and acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of theCatalyticDomain ofArabidopsis thalianaStarch Synthase IV, of Granule Bound Starch Synthase From CLg1 and of Granule Bound Starch Synthase I ofCyanophora paradoxaIllustrate Substrate Recognition in Starch Synthases.

Nielsen, M.M.Ruzanski, C.Krucewicz, K.Striebeck, A.Cenci, U.Ball, S.G.Palcic, M.M.Cuesta-Seijo, J.A.

(2018) Front Plant Sci 9: 1138-1138

  • DOI: 10.3389/fpls.2018.01138
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Starch synthases (SSs) are responsible for depositing the majority of glucoses in starch. Structural knowledge on these enzymes that is available from the crystal structures of rice granule bound starch synthase (GBSS) and barley SSI provides incompl ...

    Starch synthases (SSs) are responsible for depositing the majority of glucoses in starch. Structural knowledge on these enzymes that is available from the crystal structures of rice granule bound starch synthase (GBSS) and barley SSI provides incomplete information on substrate binding and active site architecture. Here we report the crystal structures of the catalytic domains of SSIV from Arabidopsis thaliana , of GBSS from the cyanobacterium CLg1 and GBSSI from the glaucophyte Cyanophora paradoxa , with all three bound to ADP and the inhibitor acarbose. The SSIV structure illustrates in detail the modes of binding for both donor and acceptor in a plant SS. CLg1GBSS contains, in the same crystal structure, examples of molecules with and without bound acceptor, which illustrates the conformational changes induced upon acceptor binding that presumably precede catalytic activity. With structures available from several isoforms of plant and non-plant SSs, as well as the closely related bacterial glycogen synthases, we analyze, at the structural level, the common elements that define a SS, the elements that are necessary for substrate binding and singularities of the GBSS family that could underlie its processivity. While the phylogeny of the SSIII/IV/V has been recently discussed, we now further report the detailed evolutionary history of the GBSS/SSI/SSII type of SSs enlightening the origin of the GBSS enzymes used in our structural analysis.


    Organizational Affiliation

    Carlsberg Research Laboratory, Copenhagen, Denmark.,UMR8576 CNRS-USTL, Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Villeneuve-d'Ascq, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable starch synthase 4, chloroplastic/amyloplastic
A, B
508Arabidopsis thalianaMutation(s): 0 
Gene Names: SS4
EC: 2.4.1.21
Find proteins for Q0WVX5 (Arabidopsis thaliana)
Go to UniProtKB:  Q0WVX5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 129.760α = 90.00
b = 166.940β = 90.00
c = 47.940γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
MOLREPphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Denmark--

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references