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- PDB-5y7o: Crystal structure of folding sensor region of UGGT from Thermomyc... -

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Basic information

Entry
Database: PDB / ID: 5y7o
TitleCrystal structure of folding sensor region of UGGT from Thermomyces dupontii
ComponentsUGGT
KeywordsTRANSFERASE / ENDOPLASMIC RETICULUM / QUALITY CONTROL / GLUCOSYLTRANSFERASE / FOLDING SENSOR
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein N-linked glycosylation via asparagine / unfolded protein binding / endoplasmic reticulum
Similarity search - Function
UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / UDP-glucose:Glycoprotein Glucosyltransferase
Similarity search - Domain/homology
Biological speciesThermomyces dupontii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsSatoh, T. / Song, C. / Zhu, T. / Toshimori, T. / Murata, K. / Hayashi, Y. / Kamikubo, H. / Uchihashi, T. / Kato, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25102001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25102008 Japan
Japan Science and Technology AgencyJPMJPR13L5 Japan
CitationJournal: Sci Rep / Year: 2017
Title: Visualisation of a flexible modular structure of the ER folding-sensor enzyme UGGT.
Authors: Tadashi Satoh / Chihong Song / Tong Zhu / Takayasu Toshimori / Kazuyoshi Murata / Yugo Hayashi / Hironari Kamikubo / Takayuki Uchihashi / Koichi Kato /
Abstract: In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates ...In the endoplasmic reticulum (ER), a protein quality control system facilitates the efficient folding of newly synthesised proteins. In this system, a series of N-linked glycan intermediates displayed on the protein surface serve as quality tags. The ER folding-sensor enzyme UDP-glucose:glycoprotein glucosyltransferase (UGGT) acts as a gatekeeper in the ER quality control system by specifically catalysing monoglucosylation onto incompletely folded glycoproteins, thereby enabling them to interact with lectin-chaperone complexes. Here we characterise the dynamic structure of this enzyme. Our crystallographic data demonstrate that the sensor region is composed of four thioredoxin-like domains followed by a β-rich domain, which are arranged into a C-shaped structure with a large central cavity, while the C-terminal catalytic domain undergoes a ligand-dependent conformational alteration. Furthermore, small-angle X-ray scattering, cryo-electron microscopy and high-speed atomic force microscopy have demonstrated that UGGT has a flexible modular structure in which the smaller catalytic domain is tethered to the larger folding-sensor region with variable spatial arrangements. These findings provide structural insights into the working mechanism whereby UGGT operates as a folding-sensor against a variety of glycoprotein substrates through its flexible modular structure possessing extended hydrophobic surfaces for the recognition of unfolded substrates.
History
DepositionAug 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UGGT
B: UGGT


Theoretical massNumber of molelcules
Total (without water)252,1652
Polymers252,1652
Non-polymers00
Water00
1
A: UGGT


Theoretical massNumber of molelcules
Total (without water)126,0821
Polymers126,0821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UGGT


Theoretical massNumber of molelcules
Total (without water)126,0821
Polymers126,0821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.090, 195.090, 142.260
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 UGGT


Mass: 126082.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces dupontii (fungus) / Plasmid: pCold-GST (modified) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCJ7*PLUS
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.95 M Ammonium sulfate, 0.1 M Tris-HCl (pH 7.0), 8 mM n-decanoylsucrose

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97864 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 3.1→50 Å / Num. obs: 105778 / % possible obs: 96.4 % / Redundancy: 2.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.4
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 17378 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→19.97 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.9
RfactorNum. reflection% reflection
Rfree0.2783 2744 5.02 %
Rwork0.2322 --
obs0.2352 54648 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14318 0 0 0 14318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414604
X-RAY DIFFRACTIONf_angle_d2.26919832
X-RAY DIFFRACTIONf_dihedral_angle_d17.0445402
X-RAY DIFFRACTIONf_chiral_restr0.0882284
X-RAY DIFFRACTIONf_plane_restr0.012562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1027-3.1560.43941360.41362583X-RAY DIFFRACTION94
3.156-3.21310.39031390.38472625X-RAY DIFFRACTION95
3.2131-3.27460.44821370.35592599X-RAY DIFFRACTION94
3.2746-3.34120.41781370.36112612X-RAY DIFFRACTION94
3.3412-3.41350.34211370.34392597X-RAY DIFFRACTION94
3.4135-3.49250.33691380.35682615X-RAY DIFFRACTION94
3.4925-3.57930.35271360.36332588X-RAY DIFFRACTION94
3.5793-3.67550.35771380.31062613X-RAY DIFFRACTION94
3.6755-3.7830.32371350.30282578X-RAY DIFFRACTION93
3.783-3.90420.31341380.29112606X-RAY DIFFRACTION93
3.9042-4.04260.31471340.2852546X-RAY DIFFRACTION92
4.0426-4.2030.28291360.25252575X-RAY DIFFRACTION93
4.203-4.39230.31471360.2512583X-RAY DIFFRACTION93
4.3923-4.62110.25311340.22572547X-RAY DIFFRACTION92
4.6211-4.90660.26331360.21442592X-RAY DIFFRACTION93
4.9066-5.27880.24291370.21522601X-RAY DIFFRACTION93
5.2788-5.79810.2831370.21692608X-RAY DIFFRACTION93
5.7981-6.60990.261380.21832605X-RAY DIFFRACTION93
6.6099-8.22830.23771370.17962613X-RAY DIFFRACTION93
8.2283-19.87560.19721380.13862612X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.014-0.24220.2411.50410.51351.31940.0992-0.0665-0.12510.20610.082-0.2683-0.1550.6052-0.17531.0609-0.0813-0.06960.64040.06050.602133.32662.58857.4664
21.58270.7109-1.16340.3272-0.59551.35220.2623-0.22710.1367-0.3136-0.16330.0857-0.13440.1235-0.07641.7658-0.1720.00410.65040.00680.863120.905988.57199.01
31.46870.1710.20330.51070.27212.2904-0.1811-0.03070.3395-0.4214-0.2427-0.0865-0.3465-0.1980.41091.4031-0.26760.23230.66560.01591.017713.030593.6063-32.5439
42.0596-0.21240.40871.45310.91032.20390.338-0.0154-0.05530.1517-0.26830.0374-0.25770.2433-0.16111.2574-0.18820.13210.52140.08930.756716.932579.5422-45.2879
52.25860.02170.78560.51430.36070.841-0.0836-0.07430.3532-0.04270.118-0.2822-0.43560.3031-0.1741.2999-0.28320.11540.96120.11750.974643.788189.8805-27.6436
61.46380.1405-1.48040.024-0.35541.4198-0.09730.14580.5610.23230.1257-0.0232-0.14980.1201-0.01511.5401-0.2162-0.03610.7186-0.03130.882232.716588.7607-3.8355
72.81230.5283-0.23312.46330.36590.42630.1259-0.2431-0.40110.779-0.1054-0.0775-0.38180.3385-0.03881.3953-0.0262-0.02250.68080.07520.755112.669364.296717.4989
81.01180.4369-0.5360.9002-0.15631.4117-0.0496-0.0515-0.1339-0.12680.0476-0.17050.00420.54880.0281.20080.11160.0710.74310.0290.802733.336950.2575-55.0358
90.2188-0.2027-0.163-1.0693-0.30161.2468-0.0471-0.0139-0.2137-0.127-0.11560.10070.54130.15480.10831.87830.22470.06820.7309-0.04710.834317.1321.8331-36.3468
101.2509-0.04860.47541.52040.43762.3703-0.13460.05220.041-0.33290.05340.3152-0.23390.24830.16821.27570.2097-0.10960.630.09740.686816.833333.1503-1.884
111.14510.071-0.21770.4253-0.72520.9870.012-0.0026-0.0774-0.407-0.2641-0.0268-0.05570.55910.11441.29740.3524-0.04790.99160.06060.88243.86823.3317-19.8084
121.5847-0.2131.5541.2603-0.87991.62410.36960.034-0.0247-0.0338-0.2958-0.15970.36110.2967-0.04781.39720.19740.15520.69630.04150.683432.835123.7571-43.5798
132.88250.40750.05151.42510.09360.39790.17260.22260.1217-0.0791-0.1051-0.09940.04820.159-0.03221.3070.07280.09430.6244-0.07220.715512.936248.046-64.8986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 318 )
2X-RAY DIFFRACTION2chain 'A' and (resid 319 through 389 )
3X-RAY DIFFRACTION3chain 'A' and (resid 390 through 468 )
4X-RAY DIFFRACTION4chain 'A' and (resid 469 through 634 )
5X-RAY DIFFRACTION5chain 'A' and (resid 635 through 784 )
6X-RAY DIFFRACTION6chain 'A' and (resid 785 through 959 )
7X-RAY DIFFRACTION7chain 'A' and (resid 960 through 1042 )
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 318 )
9X-RAY DIFFRACTION9chain 'B' and (resid 319 through 468 )
10X-RAY DIFFRACTION10chain 'B' and (resid 469 through 634 )
11X-RAY DIFFRACTION11chain 'B' and (resid 635 through 784 )
12X-RAY DIFFRACTION12chain 'B' and (resid 785 through 959 )
13X-RAY DIFFRACTION13chain 'B' and (resid 960 through 1042 )

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