PDBsum entry: 1wtu

Transcription factor

PDB id: 1wtu

Contents

Protein chains

99 a.a. *

* Residue conservation analysis

PDB id:

1wtu

Name:

Transcription factor

Title:

Transcription factor 1, nmr, minimized average structure

Structure:

Transcription factor 1. Chain: a, b. Synonym: tf1. Engineered: yes. Other_details: this protein is the bacillus subtilis phage spo1-encoded type ii DNA-binding protein

Source:

Bacillus phage spo1. Organism_taxid: 10685. Gene: tf1. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

1 models

Authors:

X.Jia,A.Grove,M.Ivancic,V.L.Hsu,E.P.Geiduschek,D.R.Kearns

Key ref:

X.Jia et al. (1996). Structure of the Bacillus subtilis phage SPO1-encoded type II DNA-binding protein TF1 in solution. J Mol Biol, 263, 259-268. PubMed id: 8913305 DOI: 10.1006/jmbi.1996.0573

Date:

29-Jul-96 Release date: 12-Feb-97

Protein chains

P04445  (TF1_BPSP1) -  Transcription factor 1

Seq: 99 a.a.

Struc: 99 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: regulation of transcription (2 terms)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1006/jmbi.1996.0573

J Mol Biol 263:259-268 (1996)

PubMed id: 8913305

Structure of the Bacillus subtilis phage SPO1-encoded type II DNA-binding protein TF1 in solution.

X.Jia, A.Grove, M.Ivancic, V.L.Hsu, E.P.Geiduscheck, D.R.Kearns.

ABSTRACT

The solution structure of a type II DNA-binding protein, the bacteriophage SPO1-encoded transcription factor 1 (TF1), was determined using NMR spectroscopy. Selective 2H-labeling, 13C-labeling and isotopic heterodimers were used to distinguish contacts between and within monomers of the dimeric protein. A total of 1914 distance and dihedral angle constraints derived from NMR experiments were used in structure calculations using restrained molecular dynamics and simulated annealing protocols. The ensemble of 30 calculated structures has a root-mean-square deviation (r.m.s.d.) of 0.9 A, about the average structure for the backbone atoms, and 1.2 A for all heavy-atoms of the dimeric core (helices 1 and 2) and the beta-sheets. A severe helix distortion at residues 92-93 in the middle of helix 3 is associated with r.m.s.d. of approximately 1.5 A for the helix 3 backbone. Deviations of approximately 5 A or larger are noted for the very flexible beta-ribbon arms that constitute part of a proposed DNA-binding region. A structural model of TF1 has been calculated based on the previously reported crystal structure of the homologous HU protein and this model was used as the starting structure for calculations. A comparison between the calculated average solution structure of TF1 and a solution structure of HU indicates a similarity in the dimeric core (excluding the nine amino acid residue tail) with pairwise deviations of 2 to 3 A. The largest deviations between the average structure and the HU solution structure were found in the beta-ribbon arms, as expected. A 4 A deviation is found at residue 15 of TF1 which is in a loop connecting two helical segments; it has been reported that substitution of Glu15 by Gly increases the thermostability of TF1. The homology between TF1 and other proteins of this family leads us to anticipate similar tertiary structures.

Selected figure(s)

Figure 7.
Figure 7. Superposition of the average solution structure of TF1 (green) obtained from restrained molecular dynamics calculations and the average energy-minimized solution structure of HU (red).

Figure 8.
Figure 8. The deviations of C a atoms of the average solution structure of TF1 from the average HU solution structure.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 263, 259-268) copyright 1996.

Figures were selected by an automated process.