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- EMDB-33773: Cryo-EM structure of human OGT-OGA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33773
TitleCryo-EM structure of human OGT-OGA complex
Map dataHuman OGT-OGA Complex Conformer I
Sample
  • Complex: Cryo-EM structure of human OGT-OGA complex
    • Protein or peptide: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
    • Protein or peptide: Protein O-GlcNAcase
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsO-GlcNAc transferase / O-GlcNAcase / Complex / Mutual inhibition / TRANSFERASE / TRANSFERASE-HYDROLASE complex
Function / homology
Function and homology information


glycoprotein metabolic process / protein N-acetylglucosaminyltransferase complex / hyalurononglucosaminidase activity / protein O-GlcNAc transferase / N-acetylglucosamine metabolic process / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / glycoprotein catabolic process / protein O-GlcNAcase ...glycoprotein metabolic process / protein N-acetylglucosaminyltransferase complex / hyalurononglucosaminidase activity / protein O-GlcNAc transferase / N-acetylglucosamine metabolic process / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation / protein deglycosylation / NSL complex / : / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / mitophagy / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / negative regulation of cell migration / positive regulation of translation / cell projection / beta-N-acetylglucosaminidase activity / cellular response to glucose stimulus / mitochondrial membrane / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / glutamatergic synapse / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat ...O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Acyl-CoA N-acyltransferase / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Protein O-GlcNAcase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsLu P / Liu Y / Yu H / Gao H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130053 China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of human O-GlcNAcylation enzyme pair OGT-OGA complex.
Authors: Ping Lu / Yusong Liu / Maozhou He / Ting Cao / Mengquan Yang / Shutao Qi / Hongtao Yu / Haishan Gao /
Abstract: O-GlcNAcylation is a conserved post-translational modification that attaches N-acetyl glucosamine (GlcNAc) to myriad cellular proteins. In response to nutritional and hormonal signals, O- ...O-GlcNAcylation is a conserved post-translational modification that attaches N-acetyl glucosamine (GlcNAc) to myriad cellular proteins. In response to nutritional and hormonal signals, O-GlcNAcylation regulates diverse cellular processes by modulating the stability, structure, and function of target proteins. Dysregulation of O-GlcNAcylation has been implicated in the pathogenesis of cancer, diabetes, and neurodegeneration. A single pair of enzymes, the O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), catalyzes the addition and removal of O-GlcNAc on over 3,000 proteins in the human proteome. However, how OGT selects its native substrates and maintains the homeostatic control of O-GlcNAcylation of so many substrates against OGA is not fully understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of human OGT and the OGT-OGA complex. Our studies reveal that OGT forms a functionally important scissor-shaped dimer. Within the OGT-OGA complex structure, a long flexible OGA segment occupies the extended substrate-binding groove of OGT and positions a serine for O-GlcNAcylation, thus preventing OGT from modifying other substrates. Conversely, OGT disrupts the functional dimerization of OGA and occludes its active site, resulting in the blocking of access by other substrates. This mutual inhibition between OGT and OGA may limit the futile O-GlcNAcylation cycles and help to maintain O-GlcNAc homeostasis.
History
DepositionJul 5, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33773.png

Downloads & links

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Map

FileDownload / File: emd_33773.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman OGT-OGA Complex Conformer I
Voxel sizeX=Y=Z: 0.8389 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.49846202 - 1.1075056
Average (Standard dev.)0.0052931225 (±0.037507582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map

Fileemd_33773_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_33773_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human OGT-OGA complex

EntireName: Cryo-EM structure of human OGT-OGA complex
Components
  • Complex: Cryo-EM structure of human OGT-OGA complex
    • Protein or peptide: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
    • Protein or peptide: Protein O-GlcNAcase
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of human OGT-OGA complex

SupramoleculeName: Cryo-EM structure of human OGT-OGA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase ...

MacromoleculeName: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein O-GlcNAc transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.953414 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MASSVGNVAD STEPTKRMLS FQGLMELAHR EYQAGDFEAA ERHCMQLWRQ EPDNTGVLLL LSSIHFECRR LDRSAHFSTL AIKQNPLLA EAYSNLGNVY KERGQLQEAI EHYRHALRLK PDFIDGYINL AAALVAAGDM EGAVQAYVSA LQYNPDLYCV R SDLGNLLK ...String:
MASSVGNVAD STEPTKRMLS FQGLMELAHR EYQAGDFEAA ERHCMQLWRQ EPDNTGVLLL LSSIHFECRR LDRSAHFSTL AIKQNPLLA EAYSNLGNVY KERGQLQEAI EHYRHALRLK PDFIDGYINL AAALVAAGDM EGAVQAYVSA LQYNPDLYCV R SDLGNLLK ALGRLEEAKA CYLKAIETQP NFAVAWSNLG CVFNAQGEIW LAIHHFEKAV TLDPNFLDAY INLGNVLKEA RI FDRAVAA YLRALSLSPN HAVVHGNLAC VYYEQGLIDL AIDTYRRAIE LQPHFPDAYC NLANALKEKG SVAEAEDCYN TAL RLCPTH ADSLNNLANI KREQGNIEEA VRLYRKALEV FPEFAAAHSN LASVLQQQGK LQEALMHYKE AIRISPTFAD AYSN MGNTL KEMQDVQGAL QCYTRAIQIN PAFADAHSNL ASIHKDSGNI PEAIASYRTA LKLKPDFPDA YCNLAHCLQI VCDWT DYDE RMKKLVSIVA DQLEKNRLPS VHPHHSMLYP LSHGFRKAIA ERHGNLCLDK INVLHKPPYE HPKDLKLSDG RLRVGY VSS DFGNHPTSHL MQSIPGMHNP DKFEVFCYAL SPDDGTNFRV KVMAEANHFI DLSQIPCNGK AADRIHQDGI HILVNMN GY TKGARNELFA LRPAPIQAMW LGYPGTSGAL FMDYIITDQE TSPAEVAEQY SEKLAYMPHT FFIGDHANMF PHLKKKAV I DFKSNGHIYD NRIVLNGIDL KAFLDSLPDV KIVKMKCPDG GDNADSSNTA LNMPVIPMNT IAEAVIEMIN RGQIQITIN GFSISNGLAT TQINNKAATG EEVPRTIIVT TRSQYGLPED AIVYCNFNQL YKIDPSTLQM WANILKRVPN SVLWLLRFPA VGEPNIQQY AQNMGLPQNR IIFSPVAPKE EHVRRGQLAD VCLDTPLCNG HTTGMDVLWA GTPMVTMPGE TLASRVAASQ L TCLGCLEL IAKNRQEYED IAVKLGTDLE YLKKVRGKVW KQRISSPLFN TKQYTMELER LYLQMWEHYA AGNKPDHMIK PV EVTESAH HHHHH

UniProtKB: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

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Macromolecule #2: Protein O-GlcNAcase

MacromoleculeName: Protein O-GlcNAcase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein O-GlcNAcase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.020906 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MVQKESQATL EERESELSSN PAASAGASLE PPAAPAPGED NPAGAGGAAV AGAAGGARRF LCGVVEGFYG RPWVMEQRKE LFRRLQKWE LNTYLYAPKD DYKHRMFWRE MYSVEEAEQL MTLISAAREY EIEFIYAISP GLDITFSNPK EVSTLKRKLD Q VSQFGCRS ...String:
MVQKESQATL EERESELSSN PAASAGASLE PPAAPAPGED NPAGAGGAAV AGAAGGARRF LCGVVEGFYG RPWVMEQRKE LFRRLQKWE LNTYLYAPKD DYKHRMFWRE MYSVEEAEQL MTLISAAREY EIEFIYAISP GLDITFSNPK EVSTLKRKLD Q VSQFGCRS FALLFDDIDH NMCAADKEVF SSFAHAQVSI TNEIYQYLGE PETFLFCPTE YCGTFCYPNV SQSPYLRTVG EK LLPGIEV LWTGPKVVSK EIPVESIEEV SKIIKRAPVI WDNIHANDYD QKRLFLGPYK GRSTELIPRL KGVLTNPNCE FEA NYVAIH TLATWYKSNM NGVRKDVVMT DSEDSTVSIQ IKLENEGSDE DIETDVLYSP QMALKLALTE WLQEFGVPHQ YSSR QVAHS GAKASVVDGT PLVAAPSLNA TTVVTTVYQE PIMSQGAALS GEPTTLTKEE EKKQPDEEPM DMVVEKQEET DHKND NQIL SEIVEAKMAE ELKPMDTDKE SIAESKSPEM SMQEDCISDI APMQTDEQTN KEQFVPGPNE KPLYTAEPVT LEDLQL LAD LFYLPYEHGP KGAQMLREFQ WLRANSSVVS VNCKGKDSEK IEEWRSRAAK FEEMCGLVMG MFTRLSNCAN RTILYDM YS YVWDIKSIMS MVKSFVQWLG CRSHSSAQFL IGDQEPWAFR GGLAGEFQRL LPIDGANDLF FQPPPLTPTS KVYTIRPY F PKDEASVYKI CREMYDDGVG LPFQSQPDLI GDKLVGGLLS LSLDYCFVLE DEDGICGYAL GTVDVTPFIK KCKISWIPF MQEKYTKPNG DKELSEAEKI MLSFHEEQEV LPETFLANFP SLIKMDIHKK VTDPSVAKSM MACLLSSLKA NGSRGAFCEV RPDDKRILE FYSKLGCFEI AKMEGFPKDV VILGRSL

UniProtKB: Protein O-GlcNAcase

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Macromolecule #3: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM / Uridine diphosphate

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 114543
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3pe3


Details: 1W3B, 3PE3, 5UN9
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 114543

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Atomic model buiding 1

Initial model
PDB IDChain

1w3b

chain_id: A, source_name: PDB, initial_model_type: experimental model

3pe3

chain_id: A, source_name: PDB, initial_model_type: experimental model

5un9

chain_id: A, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 146
Output model

PDB-7yeh:
Cryo-EM structure of human OGT-OGA complex

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