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Life
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Structure, Function, Diversity and Evolution of Archaeal Proteins
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Structure, Function, Diversity and Evolution of Archaeal Proteins

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (24 November 2022) | Viewed by 1396

Special Issue Editor

Dr. Michael Pyatibratov

E-Mail Website1 Website2
Guest Editor
Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia
Interests: protein structure/function relationships; archaeal and bacterial physiology; motility and signal transduction systems in archaea; molecular mechanisms of protein–protein interactions; roles of multiple subunits in formation of supramolecular structures

Special Issue Information

Dear Colleagues,

Archaea represent the third domain of life and include very different groups of microorganisms that combine bacterial and eukaryotic characteristics, as well as properties unique only to archaea. Archaea are widespread and can be found both in extreme (temperature, salinity, pH) environments and in soil, water sources, and the human gut. The purpose of this Special Issue is to highlight the biological functions and structural features of archaeal proteins. Since many archaea are extremophiles, their proteins are responsible for adaptation to harsh environmental conditions and are characterized by increased stability. Understanding the mechanisms of protein adaptations used by archaeal extremophiles will help in the use of such proteins for industrial, environmental, and biotechnological applications capable of functioning under extreme conditions. This Special Issue will collect articles on the structure and function of various archaeal protein molecules, the mechanisms of their functioning and assembly, their evolution, as well as their biotechnological applications. Experimental work using methods of molecular biology and genetics, bioinformatics, and computational methods, as well as review articles on the diversity and function of archaeal biomolecules, are welcome.

Dr. Michael Pyatibratov
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • archaeal proteomics and functional genomics
  • adaptation mechanisms in archaea
  • protein biosynthesis and modifications
  • archaeal supramolecular structures
  • bioinformatics and computational biology

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Published Papers (1 paper)

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Research

13 pages, 2806 KiB  
Article
The Roles of Coenzyme A Binding Pocket Residues in Short and Medium Chain Acyl-CoA Synthetases
by Yu Meng, Cheryl Ingram-Smith, Oly Ahmed and Kerry Smith
Life 2023, 13(8), 1643; https://doi.org/10.3390/life13081643 - 28 Jul 2023
Viewed by 929
Abstract
Short- and medium-chain acyl-CoA synthetases catalyze similar two-step reactions in which acyl substrate and ATP bind to form an enzyme-bound acyl-adenylate, then CoA binds for formation of the acyl-CoA product. We investigated the roles of active site residues in CoA binding in acetyl-CoA [...] Read more.
Short- and medium-chain acyl-CoA synthetases catalyze similar two-step reactions in which acyl substrate and ATP bind to form an enzyme-bound acyl-adenylate, then CoA binds for formation of the acyl-CoA product. We investigated the roles of active site residues in CoA binding in acetyl-CoA synthetase (Acs) and a medium-chain acyl-CoA synthetase (Macs) that uses 2-methylbutyryl-CoA. Three highly conserved residues, Arg193, Arg528, and Arg586 of Methanothermobacter thermautotrophicus Acs (AcsMt), are predicted to form important interactions with the 5′- and 3′-phosphate groups of CoA. Kinetic characterization of AcsMt variants altered at each of these positions indicates these Arg residues play a critical role in CoA binding and catalysis. The predicted CoA binding site of Methanosarcina acetivorans Macs (MacsMa) is structurally more closely related to that of 4-chlorobenzoate:coenzyme A ligase (CBAL) than Acs. Alteration of MacsMa residues Tyr460, Arg490, Tyr525, and Tyr527, which correspond to CoA binding pocket residues in CBAL, strongly affected CoA binding and catalysis without substantially affecting acyl-adenylate formation. Both enzymes discriminate between 3′-dephospho-CoA and CoA, indicating interaction between the enzyme and the 3′-phosphate group is important. Alteration of MacsMa residues Lys461 and Lys519, located at positions equivalent to AcsMt Arg528 and Arg586, respectively, had only a moderate effect on CoA binding and catalysis. Overall, our results indicate the active site architecture in AcsMt and MacsMa differs even though these enzymes catalyze mechanistically similar reactions. The significance of this study is that we have delineated the active site architecture with respect to CoA binding and catalysis in this important enzyme superfamily. Full article
(This article belongs to the Special Issue Structure, Function, Diversity and Evolution of Archaeal Proteins)
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