PDBsum entry 1yhb

DNA binding protein

PDB id: 1yhb

Contents

Protein chain

87 a.a. *

Waters ×22

* Residue conservation analysis

PDB id:

1yhb

Name:

DNA binding protein

Title:

Crystal structures of y41h and y41f mutants of gene v protein from ff phage suggest possible protein-protein interactions in gvp-ssdna complex

Structure:

Gene v protein. Chain: a. Engineered: yes

Source:

Enterobacteria phage f1. Organism_taxid: 10863

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.180

Authors:

Y.Guan,H.Zhang,R.N.H.Konings,C.W.Hilbers,T.C.Terwilliger,A.H.-J.Wang

Key ref:

Y.Guan et al. (1994). Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex. Biochemistry, 33, 7768-7778. PubMed id: 8011642 DOI: 10.1021/bi00191a004

Date:

14-Apr-94 Release date: 22-Jun-94

Protein chain

P69543  (G5P_BPF1) -  DNA-Binding protein G5P from Enterobacteria phage f1

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.?

DOI no: 10.1021/bi00191a004

Biochemistry 33:7768-7778 (1994)

PubMed id: 8011642

Crystal structures of Y41H and Y41F mutants of gene V protein from Ff phage suggest possible protein-protein interactions in the GVP-ssDNA complex.

Y.Guan, H.Zhang, R.N.Konings, C.W.Hilbers, T.C.Terwilliger, A.H.Wang.

ABSTRACT

Gene V protein (GVP) encoded by the filamentous phage Ff (M13, fl, fd) is a homodimeric protein of 87 amino acids that binds to single-stranded DNA (ssDNA) nonspecifically and cooperatively. The structure (monoclinic C2 form) of the wild-type protein has been determined and refined at 1.8-A resolution [Skinner et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 2071-2075]. The monomer structure consists of a somewhat distorted five-stranded beta-barrel core with three prominent loops: a DNA-binding loop, a dyad loop, and a dimer contact loop. The amino acid residue at position 41 plays an important role in the dimer-dimer interactions of the protein-ssDNA complex. Two Y41 mutant structures have been studied by X-ray crystallography. The Y41F GVP structure has been refined to an R-factor of 0.180 at 2.2-A resolution and is very similar to the wild-type (wt) structure (rmsd of all C alpha atoms = 0.30 A). In contrast, Y41H GVP forms a new crystal lattice in the space group P2(1)2(1)2(1) with a = 77.18 A, b = 84.17 A, and c = 28.62 A. Its structure has been solved by the molecular replacement method and refined to an R-factor of 0.170 at 2.5-A resolution. The two monomers of Y41H are crystallographically independent, and their structures remain similar to wt-GVP but with significant differences, particularly in the DNA-binding hairpin region. In both crystals, the loop (residues 36-43) that contains the Y41 residue is involved in the crystal dimer packings but in a different manner. The dimer-dimer contacts found in the wt-GVP crystal may be important for GVP aggregation in the absence of DNA. In the presence of DNA, the dimer-dimer contacts may switch to the type found in the Y41H crystal, allowing the GVP-ssDNA complex to form cooperatively. A model of the complex, consistent with existing biochemical and biophysical data, has been constructed from those crystal packing data.