8J5D

Cryo-EM structure of starch degradation complex of BAM1-LSF1-MDH


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

The LIKE SEX FOUR 1-malate dehydrogenase complex functions as a scaffold to recruit beta-amylase to promote starch degradation.

Liu, J.Wang, X.Guan, Z.Wu, M.Wang, X.Fan, R.Zhang, F.Yan, J.Liu, Y.Zhang, D.Yin, P.Yan, J.

(2023) Plant Cell 36: 194-212

  • DOI: https://doi.org/10.1093/plcell/koad259
  • Primary Citation of Related Structures:  
    8J5D

  • PubMed Abstract: 

    In plant leaves, starch is composed of glucan polymers that accumulate in chloroplasts as the products of photosynthesis during the day; starch is mobilized at night to continuously provide sugars to sustain plant growth and development. Efficient starch degradation requires the involvement of several enzymes, including β-amylase and glucan phosphatase. However, how these enzymes cooperate remains largely unclear. Here, we show that the glucan phosphatase LIKE SEX FOUR 1 (LSF1) interacts with plastid NAD-dependent malate dehydrogenase (MDH) to recruit β-amylase (BAM1), thus reconstituting the BAM1-LSF1-MDH complex. The starch hydrolysis activity of BAM1 drastically increased in the presence of LSF1-MDH in vitro. We determined the structure of the BAM1-LSF1-MDH complex by a combination of cryo-electron microscopy, crosslinking mass spectrometry, and molecular docking. The starch-binding domain of the dual-specificity phosphatase and carbohydrate-binding module of LSF1 was docked in proximity to BAM1, thus facilitating BAM1 access to and hydrolysis of the polyglucans of starch, thus revealing the molecular mechanism by which the LSF1-MDH complex improves the starch degradation activity of BAM1. Moreover, LSF1 is phosphatase inactive, and the enzymatic activity of MDH was dispensable for starch degradation, suggesting nonenzymatic scaffold functions for LSF1-MDH in starch degradation. These findings provide important insights into the precise regulation of starch degradation.


  • Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-amylase 1, chloroplastic499Arabidopsis thalianaMutation(s): 0 
Gene Names: BAM1BMY7TRBAMYAt3g23920F14O13.12
EC: 3.2.1.2
UniProt
Find proteins for Q9LIR6 (Arabidopsis thaliana)
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Go to UniProtKB:  Q9LIR6
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UniProt GroupQ9LIR6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Malate dehydrogenase, chloroplasticB,
D [auth C]
323Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g47520F1P2.70
EC: 1.1.1.37
UniProt
Find proteins for Q9SN86 (Arabidopsis thaliana)
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UniProt GroupQ9SN86
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglucan phosphatase LSF1, chloroplasticC [auth D]529Arabidopsis thalianaMutation(s): 0 
Gene Names: LSF1PTPKIS2At3g01510F4P13.6
EC: 3.1.3
UniProt
Find proteins for F4J117 (Arabidopsis thaliana)
Explore F4J117 
Go to UniProtKB:  F4J117
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UniProt GroupF4J117
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release