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PDBsum entry 2f2e
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DNA binding protein/structural genomics
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PDB id
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2f2e
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References listed in PDB file
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Key reference
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Title
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The X-Ray crystal structure of pa1607 from pseudomonas aureginosa at 1.9 a resolution--A putative transcription factor.
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Authors
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E.A.Sieminska,
X.Xu,
A.Savchenko,
D.A.Sanders.
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Ref.
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Protein Sci, 2007,
16,
543-549.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(2007,
16,
543-549)
copyright 2007.
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