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- PDB-5vvx: Structural Investigations of the Substrate Specificity of Human O... -

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Basic information

Entry
Database: PDB / ID: 5vvx
TitleStructural Investigations of the Substrate Specificity of Human O-GlcNAcase
Components
  • Lamin B1
  • Protein O-GlcNAcase
KeywordsHYDROLASE / OGA / Human O-GlcNAcase
Function / homology
Function and homology information


glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity ...glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / protein localization to nuclear envelope / lamin filament / nuclear lamina / protein O-linked glycosylation / Initiation of Nuclear Envelope (NE) Reformation / protein deglycosylation / RHOF GTPase cycle / RHOD GTPase cycle / nuclear migration / nuclear inner membrane / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / phospholipase binding / heterochromatin formation / Meiotic synapsis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / beta-N-acetylglucosaminidase activity / structural constituent of cytoskeleton / nuclear matrix / sequence-specific double-stranded DNA binding / nuclear envelope / nuclear membrane / structural molecule activity / nucleoplasm / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein ...Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Acyl-CoA N-acyltransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Protein O-GlcNAcase / Lamin-B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, B. / Jiang, J. / Li, H. / Hu, C.-W.
Funding support United States, 1items
OrganizationGrant numberCountry
UW-Madison United States
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into the substrate binding adaptability and specificity of human O-GlcNAcase.
Authors: Li, B. / Li, H. / Hu, C.W. / Jiang, J.
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Protein O-GlcNAcase
C: Protein O-GlcNAcase
B: Lamin B1
D: Lamin B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7816
Polymers118,3384
Non-polymers4422
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-38 kcal/mol
Surface area33470 Å2
Unit cell
Length a, b, c (Å)82.922, 96.222, 89.653
Angle α, β, γ (deg.)90.00, 114.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein O-GlcNAcase / / OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma- ...OGA / Beta-N-acetylglucosaminidase / Beta-N-acetylhexosaminidase / Beta-hexosaminidase / Meningioma-expressed antigen 5 / N-acetyl-beta-D-glucosaminidase / N-acetyl-beta-glucosaminidase / Nuclear cytoplasmic O-GlcNAcase and acetyltransferase / NCOAT


Mass: 57822.582 Da / Num. of mol.: 2 / Fragment: UNP residues 60-400, 553-704
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGEA5, HEXC, KIAA0679, MEA5 / Production host: Escherichia coli (E. coli)
References: UniProt: O60502, protein O-GlcNAcase, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Protein/peptide Lamin B1


Mass: 1346.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P20700*PLUS
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9. ...Details: 0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 28990 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1384 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKE

5tke


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / SU B: 19.504 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28221 1341 4.8 %RANDOM
Rwork0.19988 ---
obs0.20382 26597 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.04 Å2
2--0.05 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7063 0 28 13 7104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027280
X-RAY DIFFRACTIONr_bond_other_d0.0020.026636
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9529844
X-RAY DIFFRACTIONr_angle_other_deg1.017315375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34723.467349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.928151252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9421547
X-RAY DIFFRACTIONr_chiral_restr0.0810.21047
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217938
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021599
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1538.8843433
X-RAY DIFFRACTIONr_mcbond_other6.1538.8833432
X-RAY DIFFRACTIONr_mcangle_it9.38613.3054272
X-RAY DIFFRACTIONr_mcangle_other9.38513.3074273
X-RAY DIFFRACTIONr_scbond_it5.6299.1543847
X-RAY DIFFRACTIONr_scbond_other5.6299.1543848
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.67113.585573
X-RAY DIFFRACTIONr_long_range_B_refined12.0798320
X-RAY DIFFRACTIONr_long_range_B_other12.0828320
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.886→2.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 74 -
Rwork0.329 1040 -
obs--52.23 %

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