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- PDB-3goy: Crystal structure of human poly(adp-ribose) polymerase 14, cataly... -

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Basic information

Entry
Database: PDB / ID: 3goy
TitleCrystal structure of human poly(adp-ribose) polymerase 14, catalytic fragment in complex with an inhibitor 3-aminobenzamide
ComponentsPoly [ADP-ribose] polymerase 14
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PARP / POLY(ADP-RIBOSE) POLYMERASE / BAL-2 / SGC / STRUCTURAL GENOMICS CONSORTIUM / NAD / TRANSFERASE / Glycosyltransferase / Nucleus / Transcription / Transcription regulation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity ...positive regulation of interleukin-4-mediated signaling pathway / negative regulation of tyrosine phosphorylation of STAT protein / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / protein poly-ADP-ribosylation / negative regulation of type II interferon-mediated signaling pathway / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / NAD+ binding / positive regulation of tyrosine phosphorylation of STAT protein / nucleotidyltransferase activity / transcription corepressor activity / negative regulation of gene expression / innate immune response / enzyme binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. ...PARP-14, RNA recognition motif 2 / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-aminobenzamide / Protein mono-ADP-ribosyltransferase PARP14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKarlberg, T. / Moche, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. ...Karlberg, T. / Moche, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Biotechnol. / Year: 2012
Title: Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors.
Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. ...Authors: Wahlberg, E. / Karlberg, T. / Kouznetsova, E. / Markova, N. / Macchiarulo, A. / Thorsell, A.G. / Pol, E. / Frostell, A. / Ekblad, T. / Oncu, D. / Kull, B. / Robertson, G.M. / Pellicciari, R. / Schuler, H. / Weigelt, J.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references / Structure summary
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Sep 6, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 14
B: Poly [ADP-ribose] polymerase 14
C: Poly [ADP-ribose] polymerase 14
D: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0198
Polymers88,4744
Non-polymers5454
Water0
1
A: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2552
Polymers22,1191
Non-polymers1361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2552
Polymers22,1191
Non-polymers1361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2552
Polymers22,1191
Non-polymers1361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Poly [ADP-ribose] polymerase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2552
Polymers22,1191
Non-polymers1361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.750, 144.270, 79.700
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1532:1618 or resseq 1627:1720 )
211chain B and (resseq 1532:1618 or resseq 1627:1720 )
311chain C and (resseq 1532:1618 or resseq 1627:1720 )
411chain D and (resseq 1532:1618 or resseq 1627:1720 )

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Components

#1: Protein
Poly [ADP-ribose] polymerase 14 / PARP-14 / B aggressive lymphoma protein 2


Mass: 22118.590 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, residues 1530-1720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAL2, KIAA1268, PARP14 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: Q460N5, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-3AB / 3-aminobenzamide / 3-Aminobenzamide


Mass: 136.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N2O

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.2M Sodium-malonate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98003 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Dec 10, 2008 / Details: Focusing mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98003 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. all: 22380 / Num. obs: 22380 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.146 / Rsym value: 0.148 / Net I/σ(I): 10.2
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1657 / Rsym value: 0.678 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BLJ

3blj


Resolution: 2.8→24.558 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 1119 5 %chosen to obey the highest possible symmetry of the lattice
Rwork0.2526 ---
all0.2546 22379 --
obs0.2546 22379 98.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.715 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--25.5769 Å2-0 Å210.6742 Å2
2---12.9254 Å2-0 Å2
3---9.2231 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 40 0 5834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0070.0486001
X-RAY DIFFRACTIONf_angle_deg0.9566.1358177
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1437X-RAY DIFFRACTIONPOSITIONAL
12B1437X-RAY DIFFRACTIONPOSITIONAL0.034
13C1428X-RAY DIFFRACTIONPOSITIONAL0.032
14D1437X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.92730.39821390.33442644X-RAY DIFFRACTION99
2.9273-3.08130.34621390.31282637X-RAY DIFFRACTION98
3.0813-3.2740.35611370.28722619X-RAY DIFFRACTION98
3.274-3.52610.30791400.24642649X-RAY DIFFRACTION99
3.5261-3.87970.25691400.2352670X-RAY DIFFRACTION99
3.8797-4.43820.26221410.22252667X-RAY DIFFRACTION99
4.4382-5.58090.24781390.22322653X-RAY DIFFRACTION99
5.5809-24.55860.29471440.25292721X-RAY DIFFRACTION99
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)
10.55960.07340.1391.21440.59150.21340.0158-0.0518-0.0264-0.0729-0.21740.56-0.0338-0.16670.10891.35940.02320.03780.9904-0.10720.021318.59840.403538.5019
21.3626-0.994-0.35640.9038-0.05390.3729-0.01510.03210.33980.1530.1484-0.27260.1528-0.02160.02290.2701-0.0033-0.09630.12-0.02550.163111.41438.705477.3503
31.00361.8062-0.04084.63051.0151.89290.1381-0.0090.4179-0.8741-0.16641.303-0.1030.3720.24311.49450.1088-0.37560.84220.10610.42058.311338.205238.907
40.58860.2894-0.10911.94060.0438-0.0793-0.2498-0.02380.0416-0.29070.1460.5421-0.06230.12850.13430.2581-0.009-0.27910.00960.0670.24760.693446.395277.9648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:2000)
2X-RAY DIFFRACTION2chain B and resid 1:2000)
3X-RAY DIFFRACTION3chain C and resid 1:2000)
4X-RAY DIFFRACTION4chain D and resid 1:2000)

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