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- PDB-5diy: Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N -

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Basic information

Entry
Database: PDB / ID: 5diy
TitleThermobaculum terrenum O-GlcNAc hydrolase mutant - D120N
Components
  • Hyaluronidase
  • TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsHYDROLASE / GH84 / OGA / O-GlcNAc hydrolase / O-GlcNAcase
Function / homology
Function and homology information


positive regulation of cGAS/STING signaling pathway / carbohydrate derivative metabolic process / cardiac septum development / coronary vasculature development / aorta development / non-canonical NF-kappaB signal transduction / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / heart morphogenesis / IRAK2 mediated activation of TAK1 complex ...positive regulation of cGAS/STING signaling pathway / carbohydrate derivative metabolic process / cardiac septum development / coronary vasculature development / aorta development / non-canonical NF-kappaB signal transduction / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / heart morphogenesis / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / transforming growth factor beta receptor signaling pathway / protein serine/threonine kinase activator activity / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / beta-N-acetylglucosaminidase activity / activated TAK1 mediates p38 MAPK activation / lung development / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / positive regulation of protein serine/threonine kinase activity / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / in utero embryonic development / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / Ub-specific processing proteases / nuclear speck / endoplasmic reticulum membrane / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Hyaluronidase / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesThermobaculum terrenum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.06 Å
AuthorsOstrowski, A. / Gundogdu, M. / Ferenbach, A.T. / Lebedev, A. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT087590MA United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Evidence for a Functional O-Linked N-Acetylglucosamine (O-GlcNAc) System in the Thermophilic Bacterium Thermobaculum terrenum.
Authors: Ostrowski, A. / Gundogdu, M. / Ferenbach, A.T. / Lebedev, A.A. / van Aalten, D.M.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jul 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 2.2Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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
P: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Q: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
A: Hyaluronidase
B: Hyaluronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9016
Polymers112,4584
Non-polymers4422
Water5,350297
1
P: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
A: Hyaluronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4503
Polymers56,2292
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint2 kcal/mol
Surface area21020 Å2
MethodPISA
2
Q: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
B: Hyaluronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4503
Polymers56,2292
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint2 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.176, 52.550, 131.511
Angle α, β, γ (deg.)90.00, 122.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 / Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase ...Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase 1-binding protein 1 / TAK1-binding protein 1


Mass: 750.797 Da / Num. of mol.: 2 / Fragment: UNP residues 392-398 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15750
#2: Protein Hyaluronidase


Mass: 55478.367 Da / Num. of mol.: 2 / Mutation: D120N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobaculum terrenum (bacteria) / Gene: Tter_0116 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D1CDN2
#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


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


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 38% PEG-4000, 400 mM sodium acetate, 0.1 M Tris-HCl
PH range: 8.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.06→49.03 Å / Num. all: 237569 / Num. obs: 57769 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.5
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALEPACKdata scaling
RefinementResolution: 2.06→49.03 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.992 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23633 2923 5.1 %RANDOM
Rwork0.20054 ---
obs0.20238 54843 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.583 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å2-0.17 Å2
2--0.3 Å20 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 2.06→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7709 0 28 297 8034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197861
X-RAY DIFFRACTIONr_bond_other_d0.0020.027240
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.95610671
X-RAY DIFFRACTIONr_angle_other_deg0.908316650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05924.03402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.334151304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3121552
X-RAY DIFFRACTIONr_chiral_restr0.0650.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021900
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_it1.143.2413734
X-RAY DIFFRACTIONr_mcbond_other1.143.243733
X-RAY DIFFRACTIONr_mcangle_it1.9064.8524657
X-RAY DIFFRACTIONr_mcangle_other1.9064.8534658
X-RAY DIFFRACTIONr_scbond_it1.2453.364127
X-RAY DIFFRACTIONr_scbond_other1.2453.364128
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1364.9826015
X-RAY DIFFRACTIONr_long_range_B_refined3.5825.7329217
X-RAY DIFFRACTIONr_long_range_B_other3.5325.6769121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.114 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 208 -
Rwork0.3 4012 -
obs--98.55 %

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