PF0610, a novel winged helix-turn-helix variant possessing a rubredoxin-like Zn ribbon motif from the hyperthermophilic archaeon, Pyrococcus furiosus

Xu Wang, Han Seung Lee, Frank J. Sugar, Francis E. Jenney, Michael W W Adams, James H. Prestegard

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

PF0610, a protein from the hyperthermophile Pyrococcus furiosus, has homologues only in other archaeal species and in three species of Fe(III)-reducing bacteria. It is thought to have a helixturn-helix (HTH) domain at the N-terminus and possesses two CXXC motifs characteristic of metal binding proteins. We have determined the solution structure of the Zn-bound protein using NMR. PF0610 is a novel winged helix-turn-helix (wHTH) protein with a rubredoxin-like Zn ribbon as its W1 segment. In addition, it possesses a large number of basic residues on its surface. Clusters of basic residues can be found on both helix H3 and the metal-binding loops of W1, suggesting that it might be a DNA-binding protein. Accordingly, gel shift assays using both linear and circular DNA showed that PF0610 does bind DNA, at least in a sequence-independent fashion. Modeling the PF0610-DNA interaction based on other wHTH protein-DNA structures revealed that besides helix H3, basic residues around the second CXXC motif in the metal-binding loop could make extensive contacts with DNA. However, the bulkiness of the W1 region implies that the DNA conformation may be distorted upon PF0610 binding. PF0610 is the first protein known to have a Zn ribbon-embedded wHTH fold and, as such, has potential roles both as a metal-dependent transcription regulator and as a component of the chromosome packing system in P. furiosus. The discovery of this novel structure represents the addition of another branch to the winged HTH protein family and could contribute to our understanding of transcription regulatory processes in P. furiosus.

Original languageEnglish (US)
Pages (from-to)752-761
Number of pages10
JournalBiochemistry
Volume46
Issue number3
DOIs
StatePublished - Jan 23 2007
Externally publishedYes

Fingerprint

Rubredoxins
Pyrococcus furiosus
Archaea
Metals
DNA
Proteins
Transcription
Nucleic Acid Conformation
Circular DNA
DNA-Binding Proteins
Chromosomes
Conformations
Assays
Bacteria
Carrier Proteins
Gels
Nuclear magnetic resonance

ASJC Scopus subject areas

  • Biochemistry

Cite this

PF0610, a novel winged helix-turn-helix variant possessing a rubredoxin-like Zn ribbon motif from the hyperthermophilic archaeon, Pyrococcus furiosus. / Wang, Xu; Lee, Han Seung; Sugar, Frank J.; Jenney, Francis E.; Adams, Michael W W; Prestegard, James H.

In: Biochemistry, Vol. 46, No. 3, 23.01.2007, p. 752-761.

Research output: Contribution to journalArticle

Wang, Xu ; Lee, Han Seung ; Sugar, Frank J. ; Jenney, Francis E. ; Adams, Michael W W ; Prestegard, James H. / PF0610, a novel winged helix-turn-helix variant possessing a rubredoxin-like Zn ribbon motif from the hyperthermophilic archaeon, Pyrococcus furiosus. In: Biochemistry. 2007 ; Vol. 46, No. 3. pp. 752-761.
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