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

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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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: https://doi.org/10.3389/fpls.2018.01138
  • Primary Citation of Related Structures:  
    6GNE, 6GNF, 6GNG

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable starch synthase 4, chloroplastic/amyloplastic
A, B
508Arabidopsis thalianaMutation(s): 0 
Gene Names: SS4At4g18240T9A21.90
Find proteins for Q0WVX5 (Arabidopsis thaliana)
Explore Q0WVX5 
Go to UniProtKB:  Q0WVX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0WVX5
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, E
Glycosylation Resources
GlyTouCan:  G66431MI
GlyCosmos:  G66431MI
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Biologically Interesting Molecules (External Reference) 2 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.76α = 90
b = 166.94β = 90
c = 47.94γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary