+Open data
-Basic information
Entry | Database: PDB / ID: 8bob | ||||||
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Title | Structural basis for negative regulation of the maltose system | ||||||
Components |
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Keywords | TRANSCRIPTION / STAND / maltose system / oligomerization | ||||||
Function / homology | Function and homology information positive regulation of carbohydrate metabolic process / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / L-cysteine desulfhydrase activity / methionine biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor binding / carbohydrate metabolic process / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription ...positive regulation of carbohydrate metabolic process / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / L-cysteine desulfhydrase activity / methionine biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor binding / carbohydrate metabolic process / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | ||||||
Authors | Chai, J. / Wu, Y. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for negative regulation of the Escherichia coli maltose system. Authors: Yuang Wu / Yue Sun / Evelyne Richet / Zhifu Han / Jijie Chai / Abstract: Proteins from the signal transduction ATPases with numerous domains (STAND) family are known to play an important role in innate immunity. However, it remains less well understood how they function ...Proteins from the signal transduction ATPases with numerous domains (STAND) family are known to play an important role in innate immunity. However, it remains less well understood how they function in transcriptional regulation. MalT is a bacterial STAND that controls the Escherichia coli maltose system. Inactive MalT is sequestered by different inhibitory proteins such as MalY. Here, we show that MalY interacts with one oligomerization interface of MalT to form a 2:2 complex. MalY represses MalT activity by blocking its oligomerization and strengthening ADP-mediated MalT autoinhibition. A loop region N-terminal to the nucleotide-binding domain (NBD) of MalT has a dual role in mediating MalT autoinhibition and activation. Structural comparison shows that ligand-binding induced oligomerization is required for stabilizing the C-terminal domains and conferring DNA-binding activity. Together, our study reveals the mechanism whereby a prokaryotic STAND is inhibited by a repressor protein and offers insights into signaling by STAND transcription activators. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bob.cif.gz | 298 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bob.ent.gz | 240.7 KB | Display | PDB format |
PDBx/mmJSON format | 8bob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bob_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8bob_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8bob_validation.xml.gz | 54 KB | Display | |
Data in CIF | 8bob_validation.cif.gz | 79.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/8bob ftp://data.pdbj.org/pub/pdb/validation_reports/bo/8bob | HTTPS FTP |
-Related structure data
Related structure data | 16140MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 43684.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: malY, b1622, JW1614 / Production host: Escherichia coli (E. coli) References: UniProt: P23256, cysteine-S-conjugate beta-lyase #2: Protein | Mass: 47318.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / DH10B / Gene: malT, ECDH10B_3593 / Production host: Escherichia coli (E. coli) / References: UniProt: B1X764 #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Binary complex of MalY and MalT / Type: CELL / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176969 / Symmetry type: POINT | ||||||||||||||||||||||||
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