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1. chinaXiv:201605.01531 [pdf]

Defining the Role of Tyrosine and Rational Tuning of Oxidase Activity by Genetic Incorporation of Unnatural Tyrosine Analogs

Lv, Xiaoxuan; Li, Jiasong; Zhou, Qing; Wang, Jiangyun; Lv, Xiaoxuan; Li, Jiasong; Zhou, Qing; Wang, Jiangyun; Yu, Yang; Lu, Yi; Cui, Chang; Mukherjee, Arnab; Lu, Yi; Hosseinzadeh, Parisa; Lu, Yi; Nilges, Mark J.
Subjects: Biology >> Biophysics

While a conserved tyrosine (Tyr) is found in oxidases, the roles of phenol ring pK(a) and reduction potential in O-2 reduction have not been defined despite many years of research on numerous oxidases and their models. These issues represent major challenges in our understanding of O-2 reduction mechanism in bioenergetics. Through genetic incorporation of unnatural amino acid analogs of Tyr, with progressively decreasing pKa of the phenol ring and increasing reduction potential, in the active site of a functional model of oxidase in myoglobin, a linear dependence of both the O-2 reduction activity and the fraction of H2O formation with the pKa of the phenol ring has been established. By using these unnatural amino acids as spectroscopic probe, we have provided conclusive evidence for the location of a Tyr radical generated during reaction with H2O2, by the distinctive hyperfine splitting patterns of the halogenated tyrosines and one of its deuterated derivatives incorporated at the 33 position of the protein. These results demonstrate for the first time that enhancing the proton donation ability of the Tyr enhances the oxidase activity, allowing the Tyr analogs to augment enzymatic activity beyond that of natural Tyr.

submitted time 2016-05-12 Hits2224Downloads1255 Comment 0

2. chinaXiv:201605.01468 [pdf]

RNAcentral: an international database of ncRNA sequences

Petrov, Anton I.; Kay, Simon J. E.; Gibson, Richard; Kulesha, Eugene; Staines, Dan; Bruford, Elspeth A.; Wright, Mathew W.; Burge, Sarah; Finn, Robert D.; Kersey, Paul J.; Cochrane, Guy; Bateman, Alex; Griffiths-Jones, Sam; Harrow, Jennifer; Chan, Patricia P.; Lowe, Todd M.; Zwieb, Christian W.; Wower, Jacek; Williams, Kelly P.; Hudson, Corey M.
Subjects: Biology >> Biophysics >> Biochemistry & Molecular Biology

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

submitted time 2016-05-12 Hits1693Downloads846 Comment 0

3. chinaXiv:201605.01453 [pdf]

Crystal structure of the catalytic subunit of magnesium chelatase

Chen, Xuemin; Pu, Hua; Fang, Ying; Wang, Xiao; Zhao, Shun; Dai, Huai-En; Liu, Lin; Chen, Xuemin; Pu, Hua; Fang, Ying; Wang, Xiao; Zhao, Shun; Lin, Yajing; Gong, Weimin; Zhang, Min; Gong, Weimin
Subjects: Biology >> Biophysics

Tetrapyrroles, including haem and chlorophyll, play vital roles for various biological processes, such as respiration and photosynthesis, and their biosynthesis is critical for virtually all organisms. In photosynthetic organisms, magnesium chelatase (MgCh) catalyses insertion of magnesium into the centre of protoporphyrin IX, the branch-point precursor for both haem and chlorophyll, leading tetrapyrrole biosynthesis into the magnesium branch1,2. This reaction needs a cooperated action of the three subunits of MgCh: the catalytic subunit ChlH and two AAA(+) subunits, ChlI and ChlD ( refs 3-5). To date, the mechanism of MgCh awaits further elucidation due to a lack of high-resolution structures, especially for the similar to 150 kDa catalytic subunit. Here we report the crystal structure of ChlH from the photosynthetic cyanobacterium Synechocystis PCC 6803, solved at 2.5 angstrom resolution. The active site is buried deeply inside the protein interior, and the surrounding residues are conserved throughout evolution. This structure helps to explain the loss of function reported for the cch and gun5 mutations of the ChlH subunit, and to provide the molecular basis of substrate channelling during the magnesium-chelating process. The structure advances our understanding of the holoenzyme of MgCh, a metal chelating enzyme other than ferrochelatase.

submitted time 2016-05-12 Hits1833Downloads978 Comment 0

4. chinaXiv:201605.01451 [pdf]

A Designed Metalloenzyme Achieving the Catalytic Rate of a Native Enzyme

Liu, Xiaohong; Wang, Jiangyun; Yu, Yang; Lu, Yi; Cui, Chang; Petrik, Igor D.; Lu, Yi
Subjects: Biology >> Biophysics

Terminal oxidases catalyze four-electron reduction of oxygen to water, and the energy harvested is utilized to drive the synthesis of adenosine triphosphate. While much effort has been made to design a catalyst mimicking the function of terminal oxidases, most biomimetic catalysts have much lower activity than native oxidases. Herein we report a designed oxidase in myoglobin with an O-2 reduction rate (52 s(-1)) comparable to that of a native cytochrome (cyt) cbb(3) oxidase (SO s(-1)) under identical conditions. We achieved this goal by engineering more favorable electrostatic interactions between a functional oxidase model designed in sperm whale myoglobin and its native redox partner, cyt b(5), resulting in a 400-fold electron transfer (ET) rate enhancement. Achieving high activity equivalent to that of native enzymes in a designed metalloenzyme offers deeper insight into the roles of tunable processes such as ET in oxidase activity and enzymatic function and may extend into applications such as more efficient oxygen reduction reaction catalysts for biofuel cells.

submitted time 2016-05-12 Hits1796Downloads978 Comment 0

5. chinaXiv:201605.01433 [pdf]

Purification, crystallization and preliminary X-ray crystallographic studies of Rv3899c from Mycobacterium tuberculosis

Song, Yingjia; Li, Honglin; Bi, Lijun; Liu, Jianghui; Wang, Shihua; Liu, Jianghui; Wang, Shihua; Li, De-Feng; Wang, Da-Cheng; Bi, Lijun; Li, De-Feng; Wang, Da-Cheng; Bi, Lijun; Zhou, Jie
Subjects: Biology >> Biophysics

Rv3899c, a hypothetical protein from Mycobacterium tuberculosis that is conserved within the mycobacteria, is predicted to be secreted and has been found in culture filtrates. Here, Rv3899c has been cloned, expressed in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion method with PEG 3350 as a precipitant was used to crystallize the protein. N-terminal sequencing results showed that the amino-acid sequence of the crystallized protein began with GATAG, indicating that it is a fragment containing residues 184-410 of Rv3899c. Rv3899c(184-410) crystals exhibited the symmetry of space group P2(1)2(1)2(1), with unit-cell parameters a = 49.88, b = 54.72, c = 75.52 angstrom, = = = 90 degrees, and diffracted to a resolution of 1.90 angstrom.

submitted time 2016-05-12 Hits1505Downloads824 Comment 0

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