2GVB

REFINED SOLUTION STRUCTURE OF THE TYR 41--> HIS MUTANT OF THE M13 GENE V PROTEIN. A COMPARISON WITH THE CRYSTAL STRUCTURE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure.

Prompers, J.J.Folmer, R.H.Nilges, M.Folkers, P.J.Konings, R.N.Hilbers, C.W.

(1995) Eur.J.Biochem. 232: 506-514

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional solution structure of mutant Tyr41-->His of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13 has been refined in two stages. The first stage involved the collection of additional NOE ...

    The three-dimensional solution structure of mutant Tyr41-->His of the single-stranded DNA binding protein encoded by gene V of the filamentous bacteriophage M13 has been refined in two stages. The first stage involved the collection of additional NOE-based distance constraints, which were then used in eight cycles of back-calculations and structure calculations. The structures of the gene V protein dimers were calculated using simulated annealing, employing restrained molecular dynamics with a geometric force field. In the second stage of the refinement procedure, solvent was explicitly included during the dynamic calculations. A total of 30 structures was calculated for the protein, representing its solution structure in water. The first calculation step significantly improved the convergence of the structures, whereas the subsequent simulations in water made the structures physically more realistic. This is, for instance, illustrated by the number of hydrogen bonds formed in the molecule, which increased considerably upon going to aqueous solution. It is shown that the solution structure of the mutant gene V protein is nearly identical to the crystal structure of the wild-type molecule, except for the DNA-binding loop (residues 16-28). This antiparallel beta-hairpin is twisted and partially folded back towards the core of the protein in the NMR structure, whereas it is more extended and points away from the rest of the molecule in the X-ray structure. Unrestrained molecular dynamics calculations suggest that this latter conformation is energetically unstable in solution.


    Related Citations: 
    • The Solution Structure of the Tyr 41--> His Mutant of the Single-Stranded DNA Binding Protein Encoded by Gene V of the Filamentous Bacteriophage M13
      Folkers, P.J.M.,Nilges, M.,Folmer, R.H.A.,Konings, R.N.H.,Hilbers, C.W.
      (1994) J.Mol.Biol. 236: 229
    • Sequence-Specific H-NMR Assignment and Secondary Structure of the Tyr 41--> His Mutant of the Single-Stranded DNA Binding Protein, Gene V Protein, Encoded by the Filamentous Bacteriophage M13
      Folkers, P.J.M.,Van Duynhoven, J.P.M.,Jonker, A.J.,Harmsen, B.J.M.,Konings, R.N.H.,Hilbers, C.W.
      (1991) Eur.J.Biochem. 202: 349
    • Exploring the DNA Binding Domain of Gene V Protein Encoded by Bacteriophage M13 with the Aid of Spin-Labeled Oligonucleotides in Combination with H-NMR
      Folkers, P.J.M.,Van Duynhoven, J.P.M.,Van Lieshout, H.T.M.,Harmsen, B.J.M.,Van Boom, J.H.,Tesser, G.I.,Konings, R.N.H.,Hilbers, C.W.
      (1993) Biochemistry 32: 9407
    • Characterization of Wild-Type and Mutant M13 Gene V Proteins by Means of H-NMR
      Folkers, P.J.M.,Stassen, A.P.M.,Van Duynhoven, J.P.M.,Harmsen, B.J.M.,Konings, R.N.H.,Hilbers, C.W.
      (1991) Eur.J.Biochem. 200: 139


    Organizational Affiliation

    Nijmegen Son Research Center, University of Nijmegen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GENE V PROTEIN
A, B
87Enterobacteria phage M13Mutation(s): 0 
Gene Names: V
Find proteins for P69544 (Enterobacteria phage M13)
Go to UniProtKB:  P69544
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance