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- EMDB-16140: Structural basis for negative regulation of the maltose system -

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Basic information

Entry
Database: EMDB / ID: EMD-16140
TitleStructural basis for negative regulation of the maltose system
Map data
Sample
  • Cell: Binary complex of MalY and MalT
    • Protein or peptide: Protein MalY
    • Protein or peptide: HTH-type transcriptional regulator MalT
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsSTAND / maltose system / transcription / oligomerization
Function / homology
Function and homology information


positive regulation of carbohydrate metabolic process / cysteine-S-conjugate beta-lyase / cysteine-S-conjugate beta-lyase activity / 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 / cysteine-S-conjugate beta-lyase activity / 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 / : / 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 ...Transcriptional regulator HTH-type, MalT / 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
HTH-type transcriptional regulator MalT / Protein MalY
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsChai J / Wu Y
Funding support Germany, 1 items
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, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16140.png

Downloads & links

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Map

FileDownload / File: emd_16140.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 297.08 Å		1.06 Å/pix.
x 280 pix.
= 297.08 Å		1.06 Å/pix.
x 280 pix.
= 297.08 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.029915273 - 0.08650728
Average (Standard dev.)0.00017636201 (±0.0020181958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 297.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16140_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16140_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of MalY and MalT

EntireName: Binary complex of MalY and MalT
Components
  • Cell: Binary complex of MalY and MalT
    • Protein or peptide: Protein MalY
    • Protein or peptide: HTH-type transcriptional regulator MalT
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Binary complex of MalY and MalT

SupramoleculeName: Binary complex of MalY and MalT / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Protein MalY

MacromoleculeName: Protein MalY / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cysteine-S-conjugate beta-lyase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 43.684703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFDFSKVVDR HGTWCTQWDY VADRFGTADL LPFTISDMDF ATAPCIIEAL NQRLMHGVFG YSRWKNDEFL AAIAHWFSTQ HYTAIDSQT VVYGPSVIYM VSELIRQWSE TGEGVVIHTP AYDAFYKAIE GNQRTVMPVA LEKQADGWFC DMGKLEAVLA K PECKIMLL ...String:
MFDFSKVVDR HGTWCTQWDY VADRFGTADL LPFTISDMDF ATAPCIIEAL NQRLMHGVFG YSRWKNDEFL AAIAHWFSTQ HYTAIDSQT VVYGPSVIYM VSELIRQWSE TGEGVVIHTP AYDAFYKAIE GNQRTVMPVA LEKQADGWFC DMGKLEAVLA K PECKIMLL CSPQNPTGKV WTCDELEIMA DLCERHGVRV ISDEIHMDMV WGEQPHIPWS NVARGDWALL TSGSKSFNIP AL TGAYGII ENSSSRDAYL SALKGRDGLS SPSVLALTAH IAAYQQGAPW LDALRIYLKD NLTYIADKMN AAFPELNWQI PQS TYLAWL DLRPLNIDDN ALQKALIEQE KVAIMPGYTY GEEGRGFVRL NAGCPRSKLE KGVAGLINAI RAVR

UniProtKB: Protein MalY

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Macromolecule #2: HTH-type transcriptional regulator MalT

MacromoleculeName: HTH-type transcriptional regulator MalT / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12 / DH10B
Molecular weightTheoretical: 47.31868 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLIPSKLSRP VRLDHTVVRE RLLAKLSGAN NFRLALITSP AGYGKTTLIS QWAAGKNDIG WYSLDEGDNQ QERFASYLIA AVQQATNGH CAICETMAQK RQYASLTSLF AQLFIELAEW HSPLYLVIDD YHLITNPVIH ESMRFFIRHQ PENLTLVVLS R NLPQLGIA ...String:
MLIPSKLSRP VRLDHTVVRE RLLAKLSGAN NFRLALITSP AGYGKTTLIS QWAAGKNDIG WYSLDEGDNQ QERFASYLIA AVQQATNGH CAICETMAQK RQYASLTSLF AQLFIELAEW HSPLYLVIDD YHLITNPVIH ESMRFFIRHQ PENLTLVVLS R NLPQLGIA NLRVRDQLLE IGSQQLAFTH QEANEFFDCR LSSPIEAAES SRICDDVSGW ATALQLIALS ARQNTHSAHK SA RRLAGIN ASHLSDYLVD EVLDNVDLAT RHFLLKSAIL RSMNDALITR VTGEENGQMR LEEIERQGLF LQRMDDTGEW FCY HPLFGN FLRQRCQWEL AAELPEIHRA AAESWMAQGF PSEAIHHALA AGDALMLRDI LLNHAWSLFN HSELSLLEES LKAL PWDSL LENPAAAIAI AIIEV

UniProtKB: HTH-type transcriptional regulator MalT

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Macromolecule #3: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176969
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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