PDBsum entry 2gva

DNA-binding (viral)

PDB id: 2gva

Contents

Protein chains

87 a.a. *

* Residue conservation analysis

PDB id:

2gva

Name:

DNA-binding (viral)

Title:

Refined solution structure of the tyr 41--> his mutant of the m13 gene v protein. A comparison with the crystal structure

Structure:

Gene v protein. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Enterobacteria phage m13. Organism_taxid: 10870.

NMR struc:

30 models

Authors:

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

Key ref:

J.J.Prompers et al. (1995). Refined solution structure of the Tyr41-->His mutant of the M13 gene V protein. A comparison with the crystal structure. Eur J Biochem, 232, 506-514. PubMed id: 7556200

Date:

27-Jul-95 Release date: 15-Oct-95

Supersedes:

1gva

Protein chains

P69544  (G5P_BPM13) -  DNA-Binding protein G5P from Enterobacteria phage M13

Seq: 87 a.a.

Struc: 87 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

Eur J Biochem 232:506-514 (1995)

PubMed id: 7556200

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

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

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-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.