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- PDB-1pun: Solution Structure of the MutT Pyrophosphohydrolase Complexed wit... -

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Entry
Database: PDB / ID: 1pun
TitleSolution Structure of the MutT Pyrophosphohydrolase Complexed with Mg(2+) and 8-oxo-dGMP, a Tightly-bound Product
ComponentsMutator mutT protein
KeywordsHYDROLASE / MUTATOR PROTEIN / NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / MUTT PYROPHOSPHOHYDROLASE-METAL-PRODUCT COMPLEX
Function / homology
Function and homology information


dGDP catabolic process / 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / nucleotide-excision repair / manganese ion binding / DNA replication ...dGDP catabolic process / 8-oxo-dGTP diphosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / nucleotide-excision repair / manganese ion binding / DNA replication / DNA repair / magnesium ion binding
Similarity search - Function
Mutator MutT / : / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain ...Mutator MutT / : / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsMassiah, M.A. / Saraswat, V. / Azurmendi, H.F. / Mildvan, A.S.
Citation
Journal: Biochemistry / Year: 2003
Title: Solution structure and NH exchange studies of the MutT pyrophosphohydrolase complexed with Mg(2+) and 8-oxo-dGMP, a tightly bound product.
Authors: Massiah, M.A. / Saraswat, V. / Azurmendi, H.F. / Mildvan, A.S.
#1: Journal: Biochemistry / Year: 1997
Title: Solution Structure of the Quaternary Complex MutT-M(2+)-AMPCPP-M(2+) Complex and Mechanism of its Pyrophosphohydrolase Action
Authors: Lin, J. / Abeygunawardana, C. / Frick, D.N. / J Bessman, M. / Mildvan, A.S.
#2: Journal: Biochemistry / Year: 1995
Title: NMR Studies of the Conformations and Location of Nucleotides Bound to the E.Coli MutT Enzyme
Authors: Frick, D.N. / Weber, D.J. / Abeygunawardana, C. / Gittis, A.G. / J Bessman, M. / Mildvan, A.S.
#3: Journal: Biochemistry / Year: 1995
Title: Solution Structure of the MutT Enzyme, a Nucleoside Triphosphate Pyrophosphohydrolase
Authors: Abeygunawardana, C. / Weber, D.J. / Gittis, A.G. / Frick, D.N. / Lin, J. / Miller, A.F. / Bessman, M.J. / Mildvan, A.S.
History
DepositionJun 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mutator mutT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3333
Polymers14,9451
Non-polymers3882
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Mutator mutT protein / 7 / 8-dihydro-8-oxoguanine-triphosphatase / 8-oxo-dGTPase / dGTP pyrophosphohydrolase


Mass: 14945.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MUTT,STRAIN: K12-I7023 / Plasmid: PET MUTT, T7 PROMOTER / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174
References: UniProt: P08337, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-8OG / 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
1312D TOCSY
1413D 13C-separated NOESY
15112C/13C-filtered-NOESY-HSQC
26215N-1H IPAP-HSQC
171HNCA
181NHCACB
NMR detailsText: Sample condition 2 was used to measure residual dipolar couplings.

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Sample preparation

Details
Solution-IDContentsSolvent system
11MM MUTT, 1.3MM 8-OXO-DGMP, 15MM MGCL2, 4MM D11-TRIS-HCL, PH 7.5, 21MM NACL, 0.34MM NAN3.90% H2O/10% D2O
21MM MUTT, 1.3MM 8-OXO-DGMP, 15MM MGCL2, 4MM D11-TRIS-HCL, PH 7.5, 21MM NACL, 0.34MM NAN3.90% H2O, 10% D2O. 3% (w/v) bicelles (C8E5/octanol ratio 0.87)
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
121 mM NaCl 7.5 ambient 295 K
221 mM NaCl 7.5 ambient 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1F. Delaglioprocessing
CNS1.1A. Brunger et al.structure solution
TALOS1999.019.15.47Cornilecu, Delaglio and Baxdata analysis
CNS1.1A. Brunger et al.refinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
Details: the structures are based on 1746 NOE-derived distance constraints, 186 dihedral angle restraints derived from TALOS, 82 distance restraints from hydrogen bonds and 53 N-H residual dipolar couplings.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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