Faculty Opinions recommendation of Crystal structure of the dimeric C-terminal domain of TonB reveals a novel fold.

VqsR is a quorum-sensing (QS) transcriptional regulator which controls QS systems (las,rhlandpqs) by directly downregulating the expression ofqscRinPseudomonas aeruginosa. As a member of the LuxR family of proteins, VqsR shares the common motif of a helix–turn–helix (HTH)-type DNA-binding domain at the C-terminus, while the function of its N-terminal domain remains obscure. Here, the crystal structure of the N-terminal domain of VqsR (VqsR-N; residues 1–193) was determined at a resolution of 2.1 Å. The structure is folded into a regular α–β–α sandwich topology, which is similar to the ligand-binding domain (LBD) of the LuxR-type QS receptors. Although their sequence similarity is very low, structural comparison reveals that VqsR-N has a conserved enclosed cavity which could recognize acyl-homoserine lactones (AHLs) as in other LuxR-type AHL receptors. The structure suggests that VqsR could be a potential AHL receptor.

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The 1.8-Å Crystal Structure of the N-Terminal Domain of an Archaeal MCM as a Right-Handed Filament

Journal of Molecular Biology ◽

10.1016/j.jmb.2013.12.025 ◽

2014 ◽

Vol 426 (7) ◽

pp. 1512-1523 ◽

Cited By ~ 9

Author(s):

Yang Fu ◽

Ian M. Slaymaker ◽

Junfeng Wang ◽

Ganggang Wang ◽

Xiaojiang S. Chen

Keyword(s):

Crystal Structure ◽

Terminal Domain

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Crystal Structure of the N-terminal Domain of Ryanodine Receptor from Plutella xylostella

Journal of Visualized Experiments ◽

10.3791/58568 ◽

2018 ◽

Author(s):

Bidhan Chandra Nayak ◽

Jie Wang ◽

Lianyun Lin ◽

Weiyi He ◽

Minsheng You ◽

...

Keyword(s):

Crystal Structure ◽

Ryanodine Receptor ◽

Plutella Xylostella ◽

Terminal Domain

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Crystal Structure and Trimer-Monomer Transition of N-Terminal Domain of EhCaBP1 from Entamoeba histolytica

Biophysical Journal ◽

10.1016/j.bpj.2010.03.048 ◽

2010 ◽

Vol 98 (12) ◽

pp. 2933-2942 ◽

Cited By ~ 7

Author(s):

Shivesh Kumar ◽

Ejaz Ahmad ◽

M. Shahid Mansuri ◽

Sanjeev Kumar ◽

Ruchi Jain ◽

...

Keyword(s):

Crystal Structure ◽

Entamoeba Histolytica ◽

Terminal Domain

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Structural and biochemical characterization of bifunctional XynA

10.1101/2020.10.20.348094 ◽

2020 ◽

Author(s):

Wei Xie ◽

Qi Yu ◽

Yun Liu ◽

Ruoting Cao ◽

Ruiqing Zhang ◽

...

Keyword(s):

Crystal Structure ◽

Enzyme Activity ◽

Catalytic Mechanism ◽

Biochemical Characterization ◽

Cellulase Activity ◽

Cost Savings ◽

Site Directed Mutagenesis ◽

Enzyme Activity Assay ◽

Great Cost ◽

Terminal Domain

AbstractXylan and cellulose are the two major constituents in numerous types of lignocellulosic biomass, representing a promising resource for biofuels and other biobased industries. The efficient degradation of lignocellulose requires the synergistic actions of cellulase and xylanase. Thus, bifunctional enzyme incorporated xylanase/cellulase activity has attracted considerable attention since it has great cost savings potential. Recently, a novel GH10 family enzyme XynA identified from Bacillus sp. is found to degrade both cellulose and xylan. To understand its molecular catalytic mechanism, here we first solve the crystal structure of XynA at 2.3 Å. XynA is characterized with a classic (α/β)8 TIM-barrel fold (GH10 domain) flanked by the flexible N-terminal domain and C-terminal domain. Circular dichroism, protein thermal shift and enzyme activity assays reveal that conserved residues Glu182 and Glu280 are both important for catalytic activities of XynA, which is verified by the crystal structure of XynA with E182A/E280A double mutant. Molecular docking studies of XynA with xylohexaose and cellohexaose as well as site-directed mutagenesis and enzyme activity assay demonstrat that Gln250 and His252 are indispensible to cellulase and bifunctional activity, separately. These results elucidate the structural and biochemical features of XynA, providing clues for further modification of XynA for industrial application.

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Crystal structure of the C-terminal domain of envelope protein VP37 from white spot syndrome virus reveals sulphate binding sites responsible for heparin binding

Journal of General Virology ◽

10.1099/jgv.0.001611 ◽

2021 ◽

Vol 102 (6) ◽

Author(s):

Wasusit Somsoros ◽

Takeshi Sangawa ◽

Katsuki Takebe ◽

Jakrada Attarataya ◽

Kanokpan Wongprasert ◽

...

Keyword(s):

Crystal Structure ◽

Binding Sites ◽

Envelope Protein ◽

Molecular Mechanisms ◽

White Spot Syndrome Virus ◽

Significant Loss ◽

White Spot ◽

Heparin Binding ◽

Terminal Domain ◽

White Spot Syndrome

White spot syndrome virus (WSSV) is the most virulent pathogen causing high mortality and economic loss in shrimp aquaculture and various crustaceans. Therefore, the understanding of molecular mechanisms of WSSV infection is important to develop effective therapeutics to control the spread of this viral disease. In a previous study, we found that VP37 could bind with shrimp haemocytes through the interaction between its C-terminal domain and heparin-like molecules on the shrimp cells, and this interaction can also be inhibited by sulphated galactan. In this study, we present the crystal structure of C-terminal domain of VP37 from WSSV at a resolution of 2.51 Å. The crystal structure contains an eight-stranded β-barrel fold with an antiparallel arrangement and reveals a trimeric assembly. Moreover, there are two sulphate binding sites found in the position corresponding to R213 and K257. In order to determine whether these sulphate binding sites are involved in binding of VP37 to heparin, mutagenesis was performed to replace these residues with alanine (R213A and K257A), and the Surface Plasmon Resonance (SPR) system was used to study the interaction of each mutated VP37 with heparin. The results showed that mutants R213A and K257A exhibited a significant loss in heparin binding activity. These findings indicated that the sites of R213 and K257 on the C-terminal domain of envelope protein VP37 are essential for binding to sulphate molecules of heparin. This study provides further insight into the structure of C-terminal domain of VP37 and it is anticipated that the structure of VP37 might be used as a guideline for development of antivirus agent targeting on the VP37 protein.

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Crystal structure of the complex of the interaction domains of Escherichia coli DnaB helicase and DnaC helicase loader: structural basis implying a distortion-accumulation mechanism for the DnaB ring opening caused by DnaC binding

The Journal of Biochemistry ◽

10.1093/jb/mvz087 ◽

2019 ◽

Vol 167 (1) ◽

pp. 1-14

Author(s):

Koji Nagata ◽

Akitoshi Okada ◽

Jun Ohtsuka ◽

Takatoshi Ohkuri ◽

Yusuke Akama ◽

...

Keyword(s):

Crystal Structure ◽

Escherichia Coli ◽

Molecular Model ◽

Structural Basis ◽

Terminal Domain ◽

Helicase Dnab ◽

Accumulation Mechanism ◽

Interaction Domains ◽

Α Helix ◽

Available Information

Abstract Loading the bacterial replicative helicase DnaB onto DNA requires a specific loader protein, DnaC/DnaI, which creates the loading-competent state by opening the DnaB hexameric ring. To understand the molecular mechanism by which DnaC/DnaI opens the DnaB ring, we solved 3.1-Å co-crystal structure of the interaction domains of Escherichia coli DnaB–DnaC. The structure reveals that one N-terminal domain (NTD) of DnaC interacts with both the linker helix of a DnaB molecule and the C-terminal domain (CTD) of the adjacent DnaB molecule by forming a three α-helix bundle, which fixes the relative orientation of the two adjacent DnaB CTDs. The importance of the intermolecular interface in the crystal structure was supported by the mutational data of DnaB and DnaC. Based on the crystal structure and other available information on DnaB–DnaC structures, we constructed a molecular model of the hexameric DnaB CTDs bound by six DnaC NTDs. This model suggested that the binding of a DnaC would cause a distortion in the hexameric ring of DnaB. This distortion of the DnaB ring might accumulate by the binding of up to six DnaC molecules, resulting in the DnaB ring to open.

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