5OGU

Structure of DNA-binding HU protein from micoplasma Spiroplasma melliferum

Summary for 5OGU

• Entry DOI: 10.2210/pdb5ogu/pdb
• NMR Information: BMRB: 34163
• Descriptor: DNA-binding protein (1 entity in total)
• Functional Keywords: dna binding protein
• Biological source: Spiroplasma melliferum KC3
• Total number of polymer chains: 2
• Total formula weight: 20583.59

Authors

Altukhov, D.A.,Talyzina, A.A.,Agapova, Y.K.,Vlaskina, A.V.,Korzhenevskiy, D.A.,Bocharov, E.V.,Rakitina, T.V.,Timofeev, V.I. (deposition date: 2017-07-13, release date: 2017-08-23, Last modification date: 2024-06-19)

Primary citation

Timofeev, V.I.,Altukhov, D.A.,Talyzina, A.A.,Agapova, Y.K.,Vlaskina, A.V.,Korzhenevskiy, D.A.,Kleymenov, S.Y.,Bocharov, E.V.,Rakitina, T.V.
Structural plasticity and thermal stability of the histone-like protein from Spiroplasma melliferum are due to phenylalanine insertions into the conservative scaffold.
J.Biomol.Struct.Dyn., 36:4392-4404, 2018

PubMed Abstract: The histone-like (HU) protein is one of the major nucleoid-associated proteins of the bacterial nucleoid, which shares high sequence and structural similarity with IHF but differs from the latter in DNA-specificity. Here, we perform an analysis of structural-dynamic properties of HU protein from Spiroplasma melliferum and compare its behavior in solution to that of another mycoplasmal HU from Mycoplasma gallisepticum. The high-resolution heteronuclear NMR spectroscopy was coupled with molecular-dynamics study and comparative analysis of thermal denaturation of both mycoplasmal HU proteins. We suggest that stacking interactions in two aromatic clusters in the HUSpm dimeric interface determine not only high thermal stability of the protein, but also its structural plasticity experimentally observed as slow conformational exchange. One of these two centers of stacking interactions is highly conserved among the known HU and IHF proteins. Second aromatic core described recently in IHFs and IHF-like proteins is considered as a discriminating feature of IHFs. We performed an electromobility shift assay to confirm high affinities of HUSpm to both normal and distorted dsDNA, which are the characteristics of HU protein. MD simulations of HUSpm with alanine mutations of the residues forming the non-conserved aromatic cluster demonstrate its role in dimer stabilization, as both partial and complete distortion of the cluster enhances local flexibility of HUSpm.

PubMed: 29283021
DOI: 10.1080/07391102.2017.1417162

Experimental method

SOLUTION NMR