PDBsum entry 1vqc

DNA binding protein

PDB id

1vqc

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Contents

			Protein chain

					86 a.a. *

			Waters ×42

* Residue conservation analysis

PDB id:

1vqc

Links

Name:

DNA binding protein

Title:

Gene v protein mutant with val 35 replaced by ile 35 and ile 47 replaced by phe 47 (v35i, i47f)

Structure:

Gene v protein. Chain: a. Synonym: gvp, g5p, i35f47. Engineered: yes. Mutation: yes

Source:

Enterobacteria phage f1. Organism_taxid: 10863. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

1.80Å

R-factor:

0.218

Authors:

M.M.Skinner,T.C.Terwilliger

Key ref:

M.M.Skinner and T.C.Terwilliger (1996). Potential use of additivity of mutational effects in simplifying protein engineering. Proc Natl Acad Sci U S A, 93, 10753-10757. PubMed id: 8855252

Date:

14-Aug-96

Release date:

12-Feb-97

PROCHECK

	Headers

	References

Protein chain

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

Seq: Struc:					87 a.a. 86 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.?

[IntEnz] [ExPASy] [KEGG] [BRENDA]

	Proc Natl Acad Sci U S A 93:10753-10757 (1996)
PubMed id: 8855252

Potential use of additivity of mutational effects in simplifying protein engineering.
M.M.Skinner, T.C.Terwilliger.

ABSTRACT

The problem of rationally engineering protein molecules can be simplified where effects of mutations on protein function are additive. Crystal structures of single and double mutants in the hydrophobic core of gene V protein indicate that structural and functional effects of core mutations are additive when the regions structurally influenced by the mutations do not substantially overlap. These regions of influence can provide a simple basis for identifying sets of mutations that will show additive effects.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19535532

L.T.Huang, and M.M.Gromiha (2009).
Reliable prediction of protein thermostability change upon double mutation from amino acid sequence.

Bioinformatics, 25, 2181-2187.

17803237

A.Y.Istomin, M.M.Gromiha, O.K.Vorov, D.J.Jacobs, and D.R.Livesay (2008).
New insight into long-range nonadditivity within protein double-mutant cycles.

Proteins, 70, 915-924.

18083859

K.S.Goo, C.S.Chua, and T.S.Sim (2008).
Relevant double mutations in bioengineered Streptomyces clavuligerus deacetoxycephalosporin C synthase result in higher binding specificities which improve penicillin bioconversion.

Appl Environ Microbiol, 74, 1167-1175.

18443782

M.S.Kim, J.D.Weaver, and X.G.Lei (2008).
Assembly of mutations for improving thermostability of Escherichia coli AppA2 phytase.

Appl Microbiol Biotechnol, 79, 751-758.

16127452

A.Kun, M.Santos, and E.Szathmáry (2005).
Real ribozymes suggest a relaxed error threshold.

Nat Genet, 37, 1008-1011.

14684834

R.K.Jain, and R.Ranganathan (2004).
Local complexity of amino acid interactions in a protein core.

Proc Natl Acad Sci U S A, 101, 111-116.

PDB codes:

1q4a 1q4b 1q4c 1q4d 1q4e 1q73

11857638

B.J.McFarland, and C.Beeson (2002).
Binding interactions between peptides and proteins of the class II major histocompatibility complex.

Med Res Rev, 22, 168-203.

12163066

W.P.Russ, and R.Ranganathan (2002).
Knowledge-based potential functions in protein design.

Curr Opin Struct Biol, 12, 447-452.

10779319

C.Grosman, and A.Auerbach (2000).
Kinetic, mechanistic, and structural aspects of unliganded gating of acetylcholine receptor channels: a single-channel study of second transmembrane segment 12' mutants.

J Gen Physiol, 115, 621-635.

10779320

C.Grosman, and A.Auerbach (2000).
Asymmetric and independent contribution of the second transmembrane segment 12' residues to diliganded gating of acetylcholine receptor channels: a single-channel study with choline as the agonist.

J Gen Physiol, 115, 637-651.

10799982

T.Aita, H.Uchiyama, T.Inaoka, M.Nakajima, T.Kokubo, and Y.Husimi (2000).
Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: application to prolyl endopeptidase and thermolysin.

Biopolymers, 54, 64-79.

10535917

B.Spiller, A.Gershenson, F.H.Arnold, and R.C.Stevens (1999).
A structural view of evolutionary divergence.

Proc Natl Acad Sci U S A, 96, 12305-12310.

PDB codes:

1c00 1c7i 1c7j 1qe3 1qe8

9788353

V.Sieber, A.Plückthun, and F.X.Schmid (1998).
Selecting proteins with improved stability by a phage-based method.

Nat Biotechnol, 16, 955-960.

9266167

P.Kast, and D.Hilvert (1997).
3D structural information as a guide to protein engineering using genetic selection.

Curr Opin Struct Biol, 7, 470-479.

9098886

S.Su, Y.G.Gao, H.Zhang, T.C.Terwilliger, and A.H.Wang (1997).
Analyses of the stability and function of three surface mutants (R82C, K69H, and L32R) of the gene V protein from Ff phage by X-ray crystallography.

Protein Sci, 6, 771-780.

PDB codes:

1ae2 1ae3 1gkh 1gvp

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.