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- PDB-4nhl: Crystal structure of Tpa1p from Saccharomyces cerevisiae, termina... -

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Basic information

Entry
Database: PDB / ID: 4nhl
TitleCrystal structure of Tpa1p from Saccharomyces cerevisiae, termination and polyadenylation protein 1, in complex with N-oxalylglycine (NOG)
ComponentsPKHD-type hydroxylase TPA1
KeywordsOxidoreductase/Oxidoreductase inhibitor / 2-oxoglutarate oxygenase / oxygen sensing / protein synthesis regulation / double-stranded beta helix / jellyroll fold / prolyl hydroxylase / translation / ribosome / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of translational termination / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translational termination / regulation of translational fidelity ...peptidyl-proline di-hydroxylation / peptidyl-proline dioxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / regulation of translational termination / poly(A) binding / L-ascorbic acid binding / Protein hydroxylation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translational termination / regulation of translational fidelity / ferrous iron binding / nucleus / cytoplasm
Similarity search - Function
Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / TPA1/Ofd1, C-terminal / Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / : / Double-stranded beta-helix / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. ...Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / TPA1/Ofd1, C-terminal / Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain / Prolyl 3,4-dihydroxylase TPA1/OFD1, N-terminal domain / Oxoglutarate and iron-dependent oxygenase degradation C-term / 2OG-Fe(II) oxygenase superfamily / : / Double-stranded beta-helix / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / 4-Layer Sandwich / Jelly Rolls / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Prolyl 3,4-dihydroxylase TPA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.84 Å
AuthorsScotti, J.S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: Structure / Year: 2015
Title: Structure of the Ribosomal Oxygenase OGFOD1 Provides Insights into the Regio- and Stereoselectivity of Prolyl Hydroxylases.
Authors: Horita, S. / Scotti, J.S. / Thinnes, C. / Mottaghi-Taromsari, Y.S. / Thalhammer, A. / Ge, W. / Aik, W. / Loenarz, C. / Schofield, C.J. / McDonough, M.A.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PKHD-type hydroxylase TPA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6973
Polymers74,4951
Non-polymers2022
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.216, 67.251, 70.976
Angle α, β, γ (deg.)90.000, 105.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

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Components

#1: Protein PKHD-type hydroxylase TPA1 / Termination and polyadenylation protein 1


Mass: 74494.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: TPA1, YER049W / Plasmid: pNIC28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P40032, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8 mM MnCl2, 1.1 mM OGA, 0.1 M succinic acid, 12% PEG 3350, vapor diffusion sitting drop, temperature 293K, pH 7.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.84→30 Å / Num. all: 18339 / Num. obs: 18332 / % possible obs: 99.96 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.543 Å2 / Rmerge(I) obs: 0.178 / Χ2: 1.141 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.7 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.84-2.940.682.0618061.174100
2.94-3.060.532.7118261.263100
3.06-3.20.4393.1618091.161100
3.2-3.370.3134.4918401.169100
3.37-3.580.2256.1918121.204100
3.58-3.850.197.0818191.20899.9
3.85-4.240.1667.7418501.107100
4.24-4.850.1358.9318251.07299.7
4.85-6.10.1269.8718561.00799.9
6.1-300.07814.918891.054100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3KT7

3kt7


Resolution: 2.84→29.7 Å / Occupancy max: 1 / Occupancy min: 0.5
RfactorNum. reflectionSelection details
Rfree0.2425 1834 Random
Rwork0.181 --
obs-18325 -
Displacement parametersBiso max: 84.96 Å2 / Biso mean: 42.6496 Å2 / Biso min: 26.35 Å2
Refinement stepCycle: LAST / Resolution: 2.84→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 11 74 4453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.282
LS refinement shellResolution: 2.83→2.9 Å
RfactorNum. reflection% reflection
Rfree0.3478 125 -
Rwork0.2672 --
obs-1251 89 %

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