2GMG

Solution NMR Structure of protein PF0610 from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfG3

Summary for 2GMG

• Entry DOI: 10.2210/pdb2gmg/pdb
• NMR Information: BMRB: 7074
• Descriptor: hypothetical protein Pf0610 (1 entity in total)
• Functional Keywords: winged-helix like protein with metal binding site, structural genomics, psi, protein structure initiative, northeast structural genomics consortium, nesg, dna binding protein
• Biological source: Pyrococcus furiosus
• Total number of polymer chains: 1
• Total formula weight: 12168.45

Authors

Wang, X.,Lee, H.S.,Adams, M.W.,Northeast Structural Genomics Consortium (NESG),Montelione, G.T.,Prestegard, J.H. (deposition date: 2006-04-06, release date: 2006-11-28, Last modification date: 2024-05-01)

Primary citation

Wang, X.,Lee, H.S.,Sugar, F.J.,Jenney, F.E.,Adams, M.W.,Prestegard, J.H.
PF0610, a novel winged helix-turn-helix variant possessing a rubredoxin-like Zn ribbon motif from the hyperthermophilic archaeon, Pyrococcus furiosus.
Biochemistry, 46:752-761, 2007

PubMed 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 helix-turn-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.

PubMed: 17223696
DOI: 10.1021/bi061870h

Experimental method

SOLUTION NMR