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- PDB-9fd0: Structure of the Saccharomyces cerevisiae Pmt4-MIR domain with bo... -

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Basic information

Entry
Database: PDB / ID: 9fd0
TitleStructure of the Saccharomyces cerevisiae Pmt4-MIR domain with bound ligands
ComponentsDolichyl-phosphate-mannose--protein mannosyltransferase 4
KeywordsPEPTIDE BINDING PROTEIN / Protein O-mannosylation / glycosylation / ER luminal domain / b-trefoil / ligand binding / processivity
Function / homology
Function and homology information


dolichyl-phosphate-mannose-protein mannosyltransferase Pmt4p homodimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / regulation of endoplasmic reticulum unfolded protein response / fungal-type cell wall biogenesis / protein O-linked glycosylation via mannose / protein O-linked glycosylation / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding
Similarity search - Function
Glycosyl transferase family 39/83 / Glycosyltransferase 39-like / Protein O-mannosyl-transferase, C-terminal four TM domain / Dolichyl-phosphate-mannose-protein mannosyltransferase / C-terminal four TMM region of protein-O-mannosyltransferase / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily
Similarity search - Domain/homology
Dolichyl-phosphate-mannose--protein mannosyltransferase 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMcDowell, M.A. / Hackmann, Y. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterisation of the fungal Pmt4 homodimer.
Authors: Melanie A McDowell / Klemens Wild / Francesco Fiorentino / Daniela Bausewein / Anke Metschies / Antonella Chiapparino / Yvonne Hackmann / Florestan L Bilsing / David Brenske / Sofia ...Authors: Melanie A McDowell / Klemens Wild / Francesco Fiorentino / Daniela Bausewein / Anke Metschies / Antonella Chiapparino / Yvonne Hackmann / Florestan L Bilsing / David Brenske / Sofia Mortensen / Di Wu / Carol V Robinson / Sabine Strahl / Irmgard Sinning /
Abstract: Protein O-mannosyltransferases (PMTs) are conserved endoplasmic reticulum membrane-embedded enzymes responsible for the transfer of mannose from dolichol phosphate-mannose (Dol-P-Man) to ...Protein O-mannosyltransferases (PMTs) are conserved endoplasmic reticulum membrane-embedded enzymes responsible for the transfer of mannose from dolichol phosphate-mannose (Dol-P-Man) to serine/threonine-rich protein substrates or unfolded proteins. PMTs from three subfamilies form obligate dimers with different substrate specificities and require the concerted action of their transmembrane domains (TMDs) and a luminal MIR domain for catalysis. Here, we present structures, native mass spectrometry, and structure-based mutagenesis of the fungal Pmt4 homodimer. The core fold of the TMDs and MIR domain is conserved with the Pmt1-Pmt2 heterodimer, indicating a shared catalytic mechanism. Distinct from Pmt4, the MIR domain interacts in cis with the TMDs of the same subunit and has a β-hairpin insertion required for O-mannosylation of substrates. We further identify a cytosolic binding site for substrate Dol-P-Man within the Pmt4 TMDs, which is conserved amongst PMTs and important for in vivo activity. Thus, we provide a framework to understand the substrate specificity and regulation of the Pmt4 homodimer.
History
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1426
Polymers25,5361
Non-polymers6075
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint4 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.593, 56.767, 78.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dolichyl-phosphate-mannose--protein mannosyltransferase 4


Mass: 25535.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PMT4, YJR143C, J2176 / Production host: Escherichia coli (E. coli)
References: UniProt: P46971, dolichyl-phosphate-mannose-protein mannosyltransferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 50 mM MES pH 6, 400 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.35→45.942 Å / Num. obs: 47974 / % possible obs: 99.43 % / Redundancy: 1.9 % / CC1/2: 0.999 / Net I/σ(I): 11.11
Reflection shellResolution: 1.35→1.398 Å / Num. unique obs: 4721 / CC1/2: 0.529

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→45.942 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 1745 3.64 %
Rwork0.1525 --
obs0.1539 47968 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→45.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 39 226 2038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021866
X-RAY DIFFRACTIONf_angle_d1.6182541
X-RAY DIFFRACTIONf_dihedral_angle_d16.982679
X-RAY DIFFRACTIONf_chiral_restr0.125273
X-RAY DIFFRACTIONf_plane_restr0.013327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.38970.37241420.33863799X-RAY DIFFRACTION100
1.3897-1.43460.35741430.30423788X-RAY DIFFRACTION99
1.4346-1.48590.30661440.24713806X-RAY DIFFRACTION99
1.4859-1.54540.24151440.19433802X-RAY DIFFRACTION100
1.5454-1.61570.22631450.16153854X-RAY DIFFRACTION100
1.6157-1.70090.20581450.14263826X-RAY DIFFRACTION100
1.7009-1.80750.17421450.12493832X-RAY DIFFRACTION99
1.8075-1.9470.18431440.12053817X-RAY DIFFRACTION99
1.947-2.14290.16861460.10823842X-RAY DIFFRACTION99
2.1429-2.4530.14151460.11553889X-RAY DIFFRACTION100
2.453-3.09040.13911480.13823922X-RAY DIFFRACTION100
3.0904-45.9420.18341530.1464046X-RAY DIFFRACTION98

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