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Open data
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Basic information
Entry | Database: PDB / ID: 8j5d | ||||||
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Title | Cryo-EM structure of starch degradation complex of BAM1-LSF1-MDH | ||||||
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![]() | HYDROLASE / amylase / starch degradation | ||||||
Function / homology | ![]() chloroplast starch grain / chloroplast protein-transporting ATPase activity / starch grain / Ycf2/FtsHi complex / plastid stroma / carbohydrate phosphatase activity / protein import into chloroplast stroma / : / chloroplast inner membrane / stromule ...chloroplast starch grain / chloroplast protein-transporting ATPase activity / starch grain / Ycf2/FtsHi complex / plastid stroma / carbohydrate phosphatase activity / protein import into chloroplast stroma / : / chloroplast inner membrane / stromule / chloroplast organization / beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / starch catabolic process / protein tyrosine/serine/threonine phosphatase activity / malate dehydrogenase / embryo development ending in seed dormancy / L-malate dehydrogenase (NAD+) activity / response to water deprivation / malate metabolic process / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / plant-type vacuole / apoplast / chloroplast envelope / plastid / chloroplast stroma / dephosphorylation / tricarboxylic acid cycle / response to cold / chloroplast / defense response to bacterium / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
![]() | Guan, Z.Y. / Liu, J. / Yan, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The LIKE SEX FOUR 1-malate dehydrogenase complex functions as a scaffold to recruit β-amylase to promote starch degradation. Authors: Jian Liu / Xuecui Wang / Zeyuan Guan / Menglong Wu / Xinyue Wang / Rong Fan / Fei Zhang / Junjun Yan / Yanjun Liu / Delin Zhang / Ping Yin / Junjie Yan / ![]() 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 ...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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.6 KB | Display | ![]() |
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PDB format | ![]() | 196.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 65.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35985MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 56111.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 34120.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | | Mass: 59231.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: F4J117, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: BAM1-LSF1-MDH complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: cryoSPARC / Category: classification | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305907 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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