Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.33 kDa 
• Atom Count: 1081 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

1PPX

Solution Structure of the MutT Pyrophosphohydrolase Complexed with Mg(2+) and 8-oxo-dGMP, a Tightly-bound Product

• PDB DOI: 10.2210/pdb1PPX/pdb
• BMRB: 5866

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-17 Released: 2003-08-26 
• Deposition Author(s): Massiah, M.A., Saraswat, V., Azurmendi, H.F., Mildvan, A.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Solution structure and NH exchange studies of the MutT pyrophosphohydrolase complexed with Mg(2+) and 8-oxo-dGMP, a tightly bound product.

Massiah, M.A., Saraswat, V., Azurmendi, H.F., Mildvan, A.S.

(2003) Biochemistry 42: 10140-10154

• PubMed: 12939141 
• DOI: 10.1021/bi030105p
• Primary Citation of Related Structures:  
  1PPX, 1PUN, 1PUQ, 1PUS


• PubMed Abstract: 
  

To learn the structural basis for the unusually tight binding of 8-oxo-nucleotides to the MutT pyrophosphohydrolase of Escherichia coli (129 residues), the solution structure of the MutT-Mg(2+)-8-oxo-dGMP product complex (K(D) = 52 nM) was determined by standard 3-D heteronuclear NMR methods. Using 1746 NOEs (13.5 NOEs/residue) and 186 phi and psi values derived from backbone (15)N, Calpha, Halpha, and Cbeta chemical shifts, 20 converged structures were computed with NOE violations

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Related Citations: 

• Solution Structure of the Quaternary Complex MutT-M(2+)-AMPCPP-M(2+) Complex and Mechanism of its Pyrophosphohydrolase Action
  Lin, J., Abeygunawardana, C., Frick, D.N., J Bessman, M., Mildvan, A.S.
  (1997) Biochemistry 36: 1199

• NMR Studies of the Conformations and Location of Nucleotides Bound to the E.Coli MutT Enzyme
  Frick, D.N., Weber, D.J., Abeygunawardana, C., Gittis, A.G., J Bessman, M., Mildvan, A.S.
  (1995) Biochemistry 34: 5577

• Solution Structure of the MutT Enzyme, a Nucleoside Triphosphate Pyrophosphohydrolase
  Abeygunawardana, C., Weber, D.J., Gittis, A.G., Frick, D.N., Lin, J., Miller, A.F., Bessman, M.J., Mildvan, A.S.
  (1995) Biochemistry 34: 14997

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Organizational Affiliation: 

Department of Biological Chemistry, The Johns Hopkins School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205-2185, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mutator mutT protein	A	129	Escherichia coli	Mutation(s): 0  Gene Names: MUTT OR B0099 EC: 3.6.1 (PDB Primary Data), 3.6.1.55 (UniProt)
UniProt
Find proteins for P08337 (Escherichia coli (strain K12)) Explore P08337  Go to UniProtKB:  P08337

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8OG	C [auth A]	8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P AQIVLFLYHYFRKU-VPENINKCSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8OG	PDBBind:  1PPX	Kd: 52 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 1PPX Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-17 
• Released Date: 2003-08-26 
Deposition Author(s): Massiah, M.A., Saraswat, V., Azurmendi, H.F., Mildvan, A.S.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Database references, Derived calculations