PDBsum entry 6f5c

DNA binding protein

PDB id: 6f5c

Contents

Protein chains

110 a.a.

Ligands

_CL ×25

SO4

Waters ×200

PDB id:

6f5c

Name:

DNA binding protein

Title:

Structure of h. Salinarum rosr (vng0258) grown from nacl

Structure:

Halophilic winged-helix-turn-helix DNA binding protein. Chain: a, b. Fragment: residues 1-10 in both chains are predicted to be natively disordered. Residues 70-76 in both chains belong to the wing domain which is notoriously flexible.. Engineered: yes

Source:

Halobacterium salinarum nrc-1. Halobacterium halobium. Organism_taxid: 64091. Gene: vng_0258h. Expressed in: haloferax volcanii. Expression_system_taxid: 2246

Resolution:

1.55Å R-factor: 0.180 R-free: 0.204

Authors:

B.Shaanan,N.Kutnowski,H.Shmuely

Key ref:

N.Kutnowski et al. (2018). The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell. J Struct Biol, 204, 191-198. PubMed id: 30110657 DOI: 10.1016/j.jsb.2018.08.008

Date:

01-Dec-17 Release date: 22-Aug-18

Protein chains

Q9HSF4  (Q9HSF4_HALSA) -  PadR family transcription regulator RosR from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)

Seq: 116 a.a.

Struc: 110 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jsb.2018.08.008

J Struct Biol 204:191-198 (2018)

PubMed id: 30110657

The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.

N.Kutnowski, H.Shmuely, I.Dahan, F.Shmulevich, G.Davidov, A.Shahar, J.Eichler, R.Zarivach, B.Shaanan.

ABSTRACT

Protein-DNA interactions are highly dependent on salt concentration. To gain insight into how such interactions are maintained in the highly saline cytoplasm of halophilic archaea, we determined the 3-D structure of VNG0258H/RosR, the first haloarchaeal DNA-binding protein from the extreme halophilic archaeon Halobactrium salinarum. It is a dimeric winged-helix-turn-helix (wHTH) protein with unique features due to adaptation to the halophilic environment. As ions are major players in DNA binding processes, particularly in halophilic environments, we investigated the solution structure of the ionic envelope and located anions in the first shell around the protein in the crystal using anomalous scattering. Anions that were found to be tightly bound to residues in the positively charged DNA-binding site would probably be released upon DNA binding and will thus make significant contribution to the driving force of the binding process. Unexpectedly, ions were also found in a buried internal cavity connected to the external medium by a tunnel. Our structure lays a solid groundwork for future structural, computational and biochemical studies on complexes of the protein with cognate DNA sequences, with implications to protein-DNA interactions in hyper-saline environments.