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An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000220065-HmpCyc: Streptococcus sp. oral taxon 056 F0418 Cellular Overview Connections between pathways are omitted for legibility.

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Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Exodeoxyribonuclease III from Crenarchaeon Sulfolobus Tokodaii Strain 7
Crystal Structure Theory and Applications, 2013, 2, 155-158 Published Online December 2013 (http://www.scirp.org/journal/csta) http://dx.doi.org/10.4236/csta.2013.24021 Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Exodeoxyribonuclease III from Crenarchaeon Sulfolobus tokodaii Strain 7 Shuichi Miyamoto1*, Chieko Naoe2, Masaru Tsunoda3, Kazuo T. Nakamura2 1Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan 2School of Pharmacy, Showa University, Tokyo, Japan 3Faculty of Pharmacy, Iwaki Meisei University, Iwaki, Japan Email: *[email protected] Received October 13, 2013; revised November 12, 2013; accepted December 6, 2013 Copyright © 2013 Shuichi Miyamoto et al. This is an open access article distributed under the Creative Commons Attribution Li- cense, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT Exodeoxyribonuclease III (EXOIII) acts as a 3’→5’ exonuclease and is homologous to purinic/apyrimidinic (AP) en- donuclease (APE), which plays an important role in the base excision repair pathway. To structurally investigate the reaction and substrate recognition mechanisms of EXOIII, a crystallographic study of EXOIII from Sulfolobus tokodaii strain 7 was carried out. The purified enzyme was crystallized by using the hanging-drop vapor-diffusion method. The crystals belonged to space group C2, with unit-cell parameters a = 154.2, b = 47.7, c = 92.4 Å, β = 125.8˚ and diffracted to 1.5 Å resolution. Keywords: Crenarchaeon; Crystallization; Exodeoxyribonuclease; Sulfolobus tokodaii; X-Ray Diffraction 1. Introduction formational change upon protein binding that permits complex formation and activation of attacking water, A variety of mechanisms exist to repair damaged DNA leading to incision, in the presence of Mg2+ [10,11].
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Review Article RNA Degradation in Staphylococcus Aureus: Diversity of Ribonucleases and Their Impact
Hindawi Publishing Corporation International Journal of Genomics Volume 2015, Article ID 395753, 12 pages http://dx.doi.org/10.1155/2015/395753 Review Article RNA Degradation in Staphylococcus aureus: Diversity of Ribonucleases and Their Impact Rémy A. Bonnin and Philippe Bouloc Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, UniversiteParis-Sud,Universit´ eParis-Saclay,91400Orsay,France´ Correspondence should be addressed to Remy´ A. Bonnin; [email protected] Received 6 January 2015; Accepted 4 March 2015 Academic Editor: Martine A. Collart Copyright © 2015 R. A. Bonnin and P. Bouloc. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The regulation of RNA decay is now widely recognized as having a central role in bacterial adaption to environmental stress.Here we present an overview on the diversity of ribonucleases (RNases) and their impact at the posttranscriptional level in the human pathogen Staphylococcus aureus. RNases in prokaryotes have been mainly studied in the two model organisms Escherichia coli and Bacillus subtilis. Based on identified RNases in these two models, putative orthologs have been identified in S. aureus.Themain staphylococcal RNases involved in the processing and degradation of the bulk RNA are (i) endonucleases RNase III and RNase Y and (ii) exonucleases RNase J1/J2 and PNPase, having 5 to 3 and 3 to 5 activities, respectively. The diversity and potential roles of each RNase and of Hfq and RppH are discussed in the context of recent studies, some of which are based on next-generation sequencing technology.
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An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
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Advances in Chitin/Chitosan Characterization and Applications Edited by Marguerite Rinaudo and Francisco M. Goycoolea Printed Edition of the Special Issue Published in Polymers www.mdpi.com/journal/polymers Advances in Chitin/Chitosan Characterization and Applications Advances in Chitin/Chitosan Characterization and Applications Special Issue Editors Marguerite Rinaudo Francisco M. Goycoolea MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editors Marguerite Rinaudo Francisco M. Goycoolea University of Grenoble Alpes University of Leeds France UK Editorial Ofﬁce MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Polymers (ISSN 2073-4360) from 2017 to 2018 (available at: https://www.mdpi.com/journal/polymers/ special issues/chitin chitosan) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-802-2 (Pbk) ISBN 978-3-03897-803-9 (PDF) c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editors ..................................... ix Preface to ”Advances in Chitin/Chitosan Characterization and Applications” .........
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Pages 1–6 1ako Evolutionary trace report by report maker November 5, 2010 4.3.3 DSSP 5 4.3.4 HSSP 5 4.3.5 LaTex 5 4.3.6 Muscle 5 4.3.7 Pymol 5 4.4 Note about ET Viewer 6 4.5 Citing this work 6 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1ako): Title: Exonuclease iii from escherichia coli Compound: Mol id: 1; molecule: exonuclease iii; chain: a; ec: 3.1.11.2; engineered: yes Organism, scientiﬁc name: Escherichia Coli; 1ako contains a single unique chain 1akoA (268 residues long). 2 CHAIN 1AKOA 2.1 P09030 overview CONTENTS From SwissProt, id P09030, 100% identical to 1akoA: Description: Exodeoxyribonuclease III (EC 3.1.11.2) (Exonuclease 1 Introduction 1 III) (EXO III) (AP endonuclease VI). 2 Chain 1akoA 1 Organism, scientiﬁc name: Escherichia coli. 2.1 P09030 overview 1 Taxonomy: Bacteria; Proteobacteria; Gammaproteobacteria; 2.2 Multiple sequence alignment for 1akoA 1 Enterobacteriales; Enterobacteriaceae; Escherichia. 2.3 Residue ranking in 1akoA 1 Function: Major apurinic-apyrimidinic endonuclease of E.coli. It 2.4 Top ranking residues in 1akoA and their position on removes the damaged DNA at cytosines and guanines by cleaving the structure 2 on the 3’ side of the AP site by a beta-elimination reaction. It exhi- 2.4.1 Clustering of residues at 25% coverage. 2 bits 3’-5’-exonuclease, 3’-phosphomonoesterase, 3’-repair diesterase 2.4.2 Possible novel functional surfaces at 25% and ribonuclease H activities.
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When the Reaction Is
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letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
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