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- PDB-8uzh: SUMO fused Trehalose Synthase (TreS) of Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8uzh
TitleSUMO fused Trehalose Synthase (TreS) of Mycobacterium tuberculosis
ComponentsSUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS
KeywordsSUGAR BINDING PROTEIN / TreS / Trehalose Synthase / Mycobacterium tuberculosis / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / capsule polysaccharide biosynthetic process / Postmitotic nuclear pore complex (NPC) reformation ...maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / SUMO is proteolytically processed / SUMOylation of transcription factors / capsule polysaccharide biosynthetic process / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / alpha-amylase / glycogen biosynthetic process / alpha-amylase activity / ubiquitin-like protein ligase binding / protein sumoylation / polysaccharide catabolic process / condensed nuclear chromosome / protein tag activity / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta ...Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Glycoside hydrolase superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Trehalose synthase/amylase TreS / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPathirage, R. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI105084 United States
CitationJournal: ACS Infect Dis / Year: 2024
Title: Targeting Persistence through Inhibition of the Trehalose Catalytic Shift.
Authors: Karishma Kalera / Rachel Liu / Juhyeon Lim / Rasangi Pathirage / Daniel H Swanson / Ulysses G Johnson / Alicyn I Stothard / Jae Jin Lee / Anne W Poston / Peter J Woodruff / Donald R Ronning ...Authors: Karishma Kalera / Rachel Liu / Juhyeon Lim / Rasangi Pathirage / Daniel H Swanson / Ulysses G Johnson / Alicyn I Stothard / Jae Jin Lee / Anne W Poston / Peter J Woodruff / Donald R Ronning / Hyungjin Eoh / Benjamin M Swarts /
Abstract: Tuberculosis (TB), caused by (Mtb), is the leading cause of death worldwide by infectious disease. Treatment of Mtb infection requires a six-month course of multiple antibiotics, an extremely ...Tuberculosis (TB), caused by (Mtb), is the leading cause of death worldwide by infectious disease. Treatment of Mtb infection requires a six-month course of multiple antibiotics, an extremely challenging regimen necessitated by Mtb's ability to form drug-tolerant persister cells. Mtb persister formation is dependent on the trehalose catalytic shift, a stress-responsive metabolic remodeling mechanism in which the disaccharide trehalose is liberated from cell surface glycolipids and repurposed as an internal carbon source to meet energy and redox demands. Here, using a biofilm-persister model, metabolomics, and cryo-electron microscopy (EM), we found that azidodeoxy- and aminodeoxy-d-trehalose analogues block the Mtb trehalose catalytic shift through inhibition of trehalose synthase TreS (Rv0126), which catalyzes the isomerization of trehalose to maltose. Out of a focused eight-member compound panel constructed by chemoenzymatic synthesis, the natural product 2-trehalosamine exhibited the highest potency and significantly potentiated first- and second-line TB drugs in broth culture and macrophage infection assays. We also report the first structure of TreS bound to a substrate analogue inhibitor, obtained via cryo-EM, which revealed conformational changes likely essential for catalysis and inhibitor binding that can potentially be exploited for future therapeutic development. Our results demonstrate that inhibition of the trehalose catalytic shift is a viable strategy to target Mtb persisters and advance trehalose analogues as tools and potential adjunctive therapeutics for investigating and targeting mycobacterial persistence.
History
DepositionNov 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS
B: SUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,1945
Polymers159,0742
Non-polymers1203
Water1267
1
A: SUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS
B: SUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS
hetero molecules

A: SUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS
B: SUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,38910
Polymers318,1484
Non-polymers2406
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-1/31
Buried area12010 Å2
ΔGint-89 kcal/mol
Surface area87250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.877, 156.877, 138.436
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein SUMO fused Trehalose Synthase (TreS),Trehalose synthase/amylase TreS


Mass: 79537.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: SMT3, treS / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306, UniProt: P9WQ18
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.8 M Ammonium sulfate, 0.1 M Sodium Citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 53148 / % possible obs: 100 % / Redundancy: 21.7 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.054 / Rrim(I) all: 0.251 / Χ2: 1.77 / Net I/σ(I): 3 / Num. measured all: 1154195
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.7-2.7521.84.52526680.5890.8610.9874.6320.654
2.75-2.821.74.26626390.6280.8780.9324.3670.652
2.8-2.8521.83.81226060.650.8880.8313.9020.653
2.85-2.9121.82.97226410.7770.9350.6493.0420.672
2.91-2.9721.82.59126170.7640.9310.5652.6530.681
2.97-3.0421.81.92526570.8630.9630.421.970.704
3.04-3.1221.81.53626800.9160.9780.3351.5720.716
3.12-3.221.81.14326110.9490.9870.2491.170.769
3.2-3.321.80.83426470.9620.990.1820.8540.83
3.3-3.421.80.71826500.9770.9940.1570.7350.854
3.4-3.5221.80.51626430.9850.9960.1130.5290.902
3.52-3.6621.80.38826690.990.9970.0850.3980.926
3.66-3.8321.80.33426450.9810.9950.0730.3411.241
3.83-4.0321.80.26626450.9870.9970.0580.2731.389
4.03-4.2921.80.226500.9940.9980.0440.2051.796
4.29-4.6221.70.16926840.9920.9980.0370.1732.142
4.62-5.0821.80.14226620.9930.9980.0310.1462.114
5.08-5.8121.60.13826780.9880.9970.030.1412.77
5.81-7.3221.50.10926900.9870.9970.0240.1113.608
7.32-5020.70.08927660.9750.9940.0210.09211.391

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→43.69 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2898 1772 3.77 %
Rwork0.2476 --
obs0.2492 47062 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9687 0 3 7 9697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.614
X-RAY DIFFRACTIONf_dihedral_angle_d12.4961338
X-RAY DIFFRACTIONf_chiral_restr0.0431443
X-RAY DIFFRACTIONf_plane_restr0.0061808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.41991310.40323354X-RAY DIFFRACTION95
2.88-2.960.4051340.36873403X-RAY DIFFRACTION96
2.96-3.060.40181270.35563380X-RAY DIFFRACTION96
3.06-3.170.40761330.33963436X-RAY DIFFRACTION97
3.17-3.290.31721340.30443445X-RAY DIFFRACTION98
3.29-3.440.36791360.28973478X-RAY DIFFRACTION98
3.44-3.620.3361390.26693483X-RAY DIFFRACTION99
3.62-3.850.30881410.25553501X-RAY DIFFRACTION99
3.85-4.150.30231360.23613525X-RAY DIFFRACTION99
4.15-4.560.24851450.21313530X-RAY DIFFRACTION99
4.56-5.220.23021330.21433566X-RAY DIFFRACTION100
5.22-6.570.28591410.2433577X-RAY DIFFRACTION100
6.58-43.690.24241420.20573612X-RAY DIFFRACTION99

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