PDBsum entry 2f2e

DNA binding protein/structural genomics

PDB id: 2f2e

Contents

Protein chains

142 a.a. *

Ligands

SO4 ×4

GLC

Waters ×329

* Residue conservation analysis

PDB id:

2f2e

Name:

DNA binding protein/structural genomics

Title:

Crystal structure of pa1607, a putative transcription factor

Structure:

Pa1607. Chain: a, b. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Gene: pa1607. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.85Å R-factor: 0.181 R-free: 0.251

Authors:

E.A.Sieminska,X.Xu,H.Zheng,V.Lunin,M.Cuff,A.Joachimiak,A.Edwards, A.Savchenko,D.A.Sanders,Midwest Center For Structural Genomics (Mcsg)

Key ref:

E.A.Sieminska et al. (2007). The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor. Protein Sci, 16, 543-549. PubMed id: 17322537 DOI: 10.1110/ps.062668207

Date:

16-Nov-05 Release date: 14-Mar-06

Protein chains

Q9I3B4  (Q9I3B4_PSEAE) -  HTH hxlR-type domain-containing protein from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 146 a.a.

Struc: 142 a.a.

DOI no: 10.1110/ps.062668207

Protein Sci 16:543-549 (2007)

PubMed id: 17322537

The X-ray crystal structure of PA1607 from Pseudomonas aureginosa at 1.9 A resolution--a putative transcription factor.

E.A.Sieminska, X.Xu, A.Savchenko, D.A.Sanders.

ABSTRACT

The structure of the PA1607 protein from Pseudomonas aureginosa was determined at 1.85 A resolution using the Se-Met multiwavelength anomalous diffraction (MAD) technique. PA1607 forms a dimer and adopts a winged-helix motif similar to the MarR family of transcription regulators, though it has an unusual dimerization profile. The DNA-binding regions and a putative metal-binding site are not conserved in PA1607.

Selected figure(s)

Figure 1.
Crystal structure of PA1607. (A) Sequence alignment of PA1607 with its closest homologs (based on a BLAST search). Diagram showing the secondary structure elements in PA1607 superimposed on the sequence alignment. Aligned sequences are PA1607 (Pseudomonas aureginosa), Burkholderia cenocepacia, Rhodopseudomonas palustris, Pseudomonas fluorescens Pf-5, Shewanella baltica, and Mycobacterium tuberculosis. The blue bars represent the regions that structure alignment suggests are involved in DNA binding. (B) Stereo ribbon diagram of Pseudomonas aureginosa PA1607 dimer, color coded for monomer A (red) and monomer B (blue). [alpha]-helices ([alpha]1 --[alpha]6), [beta]-strands ([beta]1 --[beta]4), and 3[10]-helices ([eta]1) are indicated on monomer A and correspond to elements in A. Alignment figures were drawn using ESPript (Gouet et al. 1999) and other figures were made using PYMOL (Delano 2002).

Figure 2.
Structural comparison of PA1607 with other proteins. (A) Sequence alignment of PA1607 with structural homologs (based on a DALI; Holm and Sanders 1993). The alignment was carried out by aligning the structural elements in Chimera (Pettersen et al. 2004) The structural homologs are MarR (PDB code: 1JGS), a SlyA transcriptional regulator (PDB code: 1LJ9) from Enterococcus faecalis, SmtB from Synechococcus PCC7942 (PDB code: 1SMT), and OhrO (PDB code: 1Z91), a MarR-like protein from Bacillus subtilis. The colored highlighted sequence for each one represents the regions that are making dimer contacts. The blue triangles indicate the positions of residues in OhrO (1z91) that contact the DNA and the red asterisks indicate the residues that form the putative metal-binding sites in SmtB (1smt). (B) Cartoon representation of the superposition of monomer A from PA1607 with the corresponding monomers from each structure in A. The color scheme corresponds to the highlighted regions in A. Structure alignment is from DALI (Holm and Sanders 1993). (C) Stereo ribbon diagram of a superposition of PA1607 dimer with the other proteins from A. Monomer A from each of the structures was superimposed on PA1607 monomer A (as in part B) and are displayed as a colored line (color scheme as highlighted regions in A). Monomer B from each protein is then shown as a ribbon cartoon in the appropriate color for each structure. The orientation is the same as in B.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2007, 16, 543-549) copyright 2007.