The Structure of DNA-Binding Proteins from Eu- and Archaebacteria

Dijk, Jan; Reinhardt, Richard

doi:10.1007/978-3-642-71266-1_15

Cited by 29 publications

(35 citation statements)

References 37 publications

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“…The Alba proteins have been isolated from various archaea and they have distinct names, such as DBNP-B, Sac10b, Sso10b, and Ssh10b. 2,3) The new nomenclature, Alba (acetylation lowers binding affinity), 6) is used in this paper, and the prefixes Pho, Sso, Afu, and Mja are added to differentiate them from homologous proteins from P. horikoshii, S. solfataricus, Archaeoglobus fulgidus, and Methanococcus jannashii respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Alba was initially identified as 10-kDa proteins present in the chromatin of crenarchaeota, particularly in Sulfolobus species. 2,3) Subsequently, it was found that Alba homologs are present not only in crenarchaeota but also in euryarchaeota and in some eukarya. They are small, basic proteins, and they occur as a dimeric form in solution.…”

mentioning

confidence: 99%

“…2,3) Hence it was referred to as PhoAlba. In this study, to provide further structural information about euryarchaeal Alba proteins, we determined the crystal structure of PhoAlba at a resolution of 2.8 Å with molecular replacement using, the Alba structure (SsoAlba) of S. solfataricus 25) as a search model.…”

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confidence: 99%

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Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

Hada

Nakashima

Osawa

et al. 2008

Bioscience, Biotechnology, and Biochemistry

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

Hada

Nakashima

Osawa

et al. 2008

Bioscience, Biotechnology, and Biochemistry

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“…In some archaea, homologues of bacterial chromatin proteins were found in limited amounts [7]. In all archaea, small basic DNA-binding proteins were discovered in the 1980s [8], and many of them were assumed to be chromatin proteins. They were grouped into 7 kDa, 8 kDa, and 10 kDa proteins [8], and believed to be involved in *Address correspondence to these authors at the Dept.…”

Section: Introductionmentioning

confidence: 99%

“…In all archaea, small basic DNA-binding proteins were discovered in the 1980s [8], and many of them were assumed to be chromatin proteins. They were grouped into 7 kDa, 8 kDa, and 10 kDa proteins [8], and believed to be involved in *Address correspondence to these authors at the Dept. of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing 100083, China; Tel: +86-10-62334497; E-mail: jsxuan@sas.ustb.edu.cn and Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.…”

Section: Introductionmentioning

confidence: 99%

The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

Xuan¹,

Feng²

2012

CPPS

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Abstract:Here we review the present state of structural and functional studies of the Sac10b protein family, a class of highly conserved 10 kDa nucleic acid-binding proteins in archaea. Based on biochemical and structural studies, these proteins were originally assigned a role in the structural organization of chromatin; Sac10b proteins of hyperthermophilic archaea, for example, showed tight, unspecific DNA binding. More recently, however, Sac10b proteins of mesophilic archaea were found to interact preferentially with specific DNA sequences thereby affecting the expression of distinct genes. Furthermore, Sac10b proteins of hyperthermophilic, thermophilic and mesophilic archaea were also shown to bind to RNA with distinct affinities and specificities but functional consequences of RNA binding of these proteins, besides perhaps RNA stabilization, have not yet been observed. To better understand the physiological meaning of the various interactions of Sac10b proteins with nucleic acids, future work should concentrate on elucidating the molecular structures of complexes of Sac10b proteins of hyperthermophilic and mesophilic archaea with DNA and RNA. In addition, existing and new X-ray and NMR structures of individual hyperthermophilic Sac10b proteins may represent very good models for introducing thermostability especially in enzymes for industrial use.

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Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

Zhang

Zheng

2017

Biopolymers

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The hyperthermophilic Ssh10b from Sulfolobus shibatae is a member of the Sac10b family, which binds RNA in vivo as a physiological substrate, and it has been postulated to play a key role in chromosomal organization in Archaea. Even though the crystal structure of Ssh10b-RNA was resolved successively by X-ray diffraction (Protein Data Bank [PDB] code: 3WBM), the detailed dynamic characteristics of Ssh10b-RNA are still unclear. In this study, molecular dynamics (MDs) simulations at 6 temperatures (300, 350, 375, 400, 450, and 500 K) and molecular mechanics Generalized-Born surface area (MM-GB/SA) free energy calculations were performed to investigate the mechanism of how Ssh10b protects and stabilizes RNA. The simulation results indicate that RNA is stabilized by Ssh10b when the temperature rises up to 375 K. RNA is found to undergo conformational transition between A-RNA and A 0 -RNA when Ssh10b binds to RNA at 3 different temperatures (300, 350, and 375 K). Salt bridges, hydrogen bonds and hydrophobic interactions are observed, and some residues have significant impact on the structural stability of the complex. This study increases our understanding of the dynamics and interaction mechanism of hyperthermophilic proteins and RNA at the atomic level, and offers a model for studying the structural biology of hyperthermophilic proteins and RNA. K E Y W O R D Shyperthermophilic proteins, molecular dynamics, MM-GB/SA, RNA, Ssh10b

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The Structure of DNA-Binding Proteins from Eu- and Archaebacteria

Cited by 29 publications

References 37 publications

Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

Crystal Structure and Functional Analysis of an Archaeal Chromatin Protein Alba from the Hyperthermophilic ArchaeonPyrococcus horikoshiiOT3

The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

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