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- PDB-2gaf: Crystal Structure of the Vaccinia Polyadenylate Polymerase Hetero... -

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Basic information

Entry
Database: PDB / ID: 2gaf
TitleCrystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form)
Components
  • Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
  • Poly(A) polymerase catalytic subunit
KeywordsTRANSFERASE / polyadenylate polymerase / pox virus / nucleotidyltransferase / heterodimer / processivity
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding ...regulation of mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / mRNA processing / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain ...Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase C-terminal domain / Poxvirus poly(A) polymerase N-terminal domain / mRNA methyltransferase-like / Poxvirus/kinetoplastid-type cap-specific nucleoside 2-O-methyltransferase / Poxvirus cap-specific nucleoside 2-O-methyltransferase / Poly A polymerase regulatory subunit / Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile. / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta Polymerase; domain 2 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase / Poly(A) polymerase catalytic subunit / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsMoure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A.
CitationJournal: Mol.Cell / Year: 2006
Title: Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity.
Authors: Moure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A.
History
DepositionMar 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
D: Poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)89,4472
Polymers89,4472
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-4 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.085, 91.260, 133.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase / PolyA / polymerase regulatory subunit / PolyA / polymerase small subunit / PAP-S / VP39


Mass: 35057.910 Da / Num. of mol.: 1 / Mutation: R140A, K142A, R143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P07617, UniProt: Q1PIV4*PLUS, methyltransferase cap1
#2: Protein Poly(A) polymerase catalytic subunit / PolyA / polymerase large subunit / PAP-L / VP55


Mass: 54388.844 Da / Num. of mol.: 1 / Mutation: L36S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta
References: UniProt: P23371, polynucleotide adenylyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 20% PEG 4000, 0.24 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791, 0.9793
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 25, 2004
RadiationMonochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
ReflectionResolution: 2.3→500 Å / Num. all: 33681 / Num. obs: 33681 / % possible obs: 83.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.26→2.34 Å / % possible all: 68.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1380 4.1 %RANDOM
Rwork0.243 ---
all0.245 28203 --
obs0.245 28203 83.6 %-
Solvent computationBsol: 46.726 Å2
Displacement parametersBiso mean: 40.851 Å2
Baniso -1Baniso -2Baniso -3
1--0.582 Å20 Å20 Å2
2--11.715 Å20 Å2
3----11.133 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6011 0 0 140 6151
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00828
X-RAY DIFFRACTIONc_angle_deg1.416
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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