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 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report



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:  
    6GNF, 6GNE, 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 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable starch synthase 4, chloroplastic/amyloplasticA, B508Arabidopsis thalianaMutation(s): 0 
Gene Names: SS4At4g18240T9A21.90
EC: 2.4.1.21
Find proteins for Q0WVX5 (Arabidopsis thaliana)
Explore Q0WVX5 
Go to UniProtKB:  Q0WVX5
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C, E
3 N/A N/A
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
D
2 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-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 
  • 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
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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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
    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