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- PDB-8bob: Structural basis for negative regulation of the maltose system -

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Basic information

Entry
Database: PDB / ID: 8bob
TitleStructural basis for negative regulation of the maltose system
Components
  • HTH-type transcriptional regulator MalT
  • Protein MalY
KeywordsTRANSCRIPTION / 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 / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / protein homodimerization activity ...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 / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / ATP binding
Similarity search - Function
Transcriptional regulator HTH-type, MalT / MalT-like TPR region / MalT-like TPR region / : / Putative C-S lyase / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon ...Transcriptional regulator HTH-type, MalT / MalT-like TPR region / MalT-like TPR region / : / Putative C-S lyase / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Tetratricopeptide-like helical domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / HTH-type transcriptional regulator MalT / Protein MalY
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsChai, J. / Wu, Y.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
CitationJournal: 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
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.0Oct 18, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 18, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Oct 18, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 18, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 18, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 18, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 18, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 18, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein MalY
B: Protein MalY
C: HTH-type transcriptional regulator MalT
D: HTH-type transcriptional regulator MalT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,3558
Polymers182,0074
Non-polymers1,3494
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, after incubation, MalY and MalT form a complex of about 300 kDa, consistent with a heterotetrameric assembly
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10630 Å2
ΔGint-53 kcal/mol
Surface area63100 Å2
MethodPISA

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Components

#1: Protein Protein MalY


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 HTH-type transcriptional regulator MalT / ATP-dependent transcriptional activator MalT


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 ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Binary complex of MalY and MalT / Type: CELL / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176969 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00913028
ELECTRON MICROSCOPYf_angle_d0.8117724
ELECTRON MICROSCOPYf_dihedral_angle_d7.3397724
ELECTRON MICROSCOPYf_chiral_restr0.0491962
ELECTRON MICROSCOPYf_plane_restr0.0042276

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