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- PDB-2rf5: Crystal structure of human tankyrase 1- catalytic PARP domain -

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Basic information

Entry
Database: PDB / ID: 2rf5
TitleCrystal structure of human tankyrase 1- catalytic PARP domain
ComponentsTankyrase-1
KeywordsTRANSFERASE / CATALYTIC FRAGMENT / PARP / Structural Genomics / Structural Genomics Consortium / SGC / ADP-ribosylation / ANK repeat / Chromosomal protein / Glycosyltransferase / Golgi apparatus / Membrane / mRNA transport / NAD / Nuclear pore complex / Nucleus / Phosphorylation / Protein transport / Telomere / Translocation / Transport
Function / homology
Function and homology information


negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material ...negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / spindle assembly / mRNA transport / nuclear pore / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / peptidyl-threonine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell division / Golgi membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Lehtio, L. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Welin, M. / Weigelt, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Zinc binding catalytic domain of human tankyrase 1.
Authors: Lehtio, L. / Collins, R. / van den Berg, S. / Johansson, A. / Dahlgren, L.G. / Hammarstrom, M. / Helleday, T. / Holmberg-Schiavone, L. / Karlberg, T. / Weigelt, J.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_conn.ptnr2_label_seq_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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5753
Polymers29,4171
Non-polymers1582
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.950, 81.240, 82.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsAuthors state that the asymmetric unit is a biological monomer of this domain.

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Components

#1: Protein Tankyrase-1 / / TANK1 / Tankyrase I / TNKS-1 / TRF1- interacting ankyrin-related ADP-ribose polymerase


Mass: 29417.082 Da / Num. of mol.: 1 / Fragment: PARP catalytic domain: Residues 1091-1325 / Mutation: M1266I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta2 / References: UniProt: O95271, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 18% PEG 3350, 0.18M Mg formate, 3% Hexanediol, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97981 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 12043 / Num. obs: 12043 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 13.39
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.21 / Num. unique all: 1448 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PQF

2pqf


Resolution: 2.3→19.44 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.238 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC AND TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25047 968 8 %RANDOM
Rwork0.19255 ---
all0.1971 12043 --
obs0.1971 12043 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20 Å2
2---0.59 Å20 Å2
3---2.65 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 7 96 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211710
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9332297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6825205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71223.07791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62715290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5891514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021335
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2684
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21115
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.51056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21421632
X-RAY DIFFRACTIONr_scbond_it1.7953738
X-RAY DIFFRACTIONr_scangle_it2.7514.5665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 71 -
Rwork0.2 823 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.39480.23810.32121.4287-0.3461.3436-0.12250.00030.16380.14560.030.0145-0.0046-0.0330.0925-0.02680.00870.0165-0.0742-0.0023-0.0868-19.2468-12.4699-13.8911
27.4513-1.3108-2.87595.5287-0.16354.29060.00340.7406-0.243-0.263-0.1231-0.28110.2547-0.16380.1197-0.0479-0.0075-0.0231-0.0351-0.02-0.0666-11.7528-23.6444-20.4242
33.64660.06091.52811.57310.65762.1266-0.00360.4249-0.1479-0.0584-0.01250.07970.21410.05830.0161-0.0603-0.03920.0198-0.0230.0121-0.1347-25.0308-18.3076-26.0177
42.91390.1284-0.40331.30540.26380.5458-0.11180.33830.1381-0.13680.0667-0.11230.0243-0.03520.0451-0.0219-0.0176-0.0057-0.03240.0461-0.0631-11.8825-10.7275-21.9028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1104 - 118837 - 121
2X-RAY DIFFRACTION2AA1189 - 1212122 - 145
3X-RAY DIFFRACTION3AA1213 - 1252146 - 185
4X-RAY DIFFRACTION4AA1253 - 1282186 - 215
5X-RAY DIFFRACTION4AA1287 - 1314220 - 247

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