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- PDB-1tum: MUTT PYROPHOSPHOHYDROLASE-METAL-NUCLEOTIDE-METAL COMPLEX, NMR, 16... -

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Basic information

Entry
Database: PDB / ID: 1tum
TitleMUTT PYROPHOSPHOHYDROLASE-METAL-NUCLEOTIDE-METAL COMPLEX, NMR, 16 STRUCTURES
ComponentsMUTATOR MUTT PROTEIN
KeywordsMUTATOR PROTEIN / QUATERNARY COMPLEX / NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE / MUTT PYROPHOSPHOHYDROLASE-METAL-SUBSTRATE ANALOG 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain ...Mutator MutT / : / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / COBALT TETRAAMMINE ION / 8-oxo-dGTP diphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsLin, J. / Abeygunawardana, C. / Frick, D.N. / Bessman, M.J. / Mildvan, A.S.
Citation
Journal: Biochemistry / Year: 1997
Title: Solution structure of the quaternary MutT-M2+-AMPCPP-M2+ complex and mechanism of its pyrophosphohydrolase action.
Authors: Lin, J. / Abeygunawardana, C. / Frick, D.N. / Bessman, M.J. / Mildvan, A.S.
#1: 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. / Bessman, M.J. / Mildvan, A.S.
#2: 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
DepositionDec 5, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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)15,6024
Polymers14,9451
Non-polymers6573
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / -
Representative

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Components

#1: Protein MUTATOR MUTT PROTEIN / MUTTQC / DGTP PYROPHOSPHOHYDROLASE / 7 / 8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE


Mass: 14945.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MUTT-MG(2+)-AMPCPP-MG(2+) COMPLEX / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12-I7023 / Plasmid: PET MUTT, T7 PROMOTER / Gene (production host): MUTT / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3)
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-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CON / COBALT TETRAAMMINE ION


Mass: 127.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH12N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 7.6 / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 16

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