DOCSLIB.ORG

2Jgu Lichtarge Lab 2006

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
2Jgu Lichtarge Lab 2006 Pages 1–12 2jgu Evolutionary trace report by report maker July 23, 2010 4.3.1 Alistat 11 4.3.2 CE 11 4.3.3 DSSP 11 4.3.4 HSSP 11 4.3.5 LaTex 11 4.3.6 Muscle 11 4.3.7 Pymol 12 4.4 Note about ET Viewer 12 4.5 Citing this work 12 4.6 About report maker 12 4.7 Attachments 12 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2jgu): Title: Crystal structure of dna-directed dna polymerase Compound: Mol id: 1; molecule: dna polymerase; synonym: pfu polymerase, dna polymerase pfu; chain: a; ec: 2.7.7.7; engineered: yes Organism, scientific name: Pyrococcus Furiosus 2jgu contains a single unique chain 2jguA (712 residues long). CONTENTS 2 CHAIN 2JGUA 1 Introduction 1 2.1 P61876 overview 2 Chain 2jguA 1 From SwissProt, id P61876, 90% identical to 2jguA: 2.1 P61876 overview 1 Description: DNA polymerase (EC 2.7.7.7) (Pwo polymerase). 2.2 Multiple sequence alignment for 2jguA 1 Organism, scientific name: Pyrococcus woesei. 2.3 Residue ranking in 2jguA 1 Taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococca- 2.4 Top ranking residues in 2jguA and their position on les; Thermococcaceae; Pyrococcus. the structure 2 Function: In addition to polymerase activity, this DNA polymerase 2.4.1 Clustering of residues at 25% coverage. 2 exhibits 3’ to 5’ exonuclease activity. 2.4.2 Overlap with known functional surfaces at Catalytic activity: Deoxynucleoside triphosphate + DNA(n) = 25% coverage. 3 diphosphate + DNA(n+1). 2.4.3 Possible novel functional surfaces at 25% Subunit: Monomer. coverage. 4 Similarity: Belongs to the DNA polymerase type-B family. About: This Swiss-Prot entry is copyright. It is produced through a 3 Notes on using trace results 10 collaboration between the Swiss Institute of Bioinformatics and the 3.1 Coverage 10 EMBL outstation - the European Bioinformatics Institute. There are 3.2 Known substitutions 10 no restrictions on its use as long as its content is in no way modified 3.3 Surface 10 and this statement is not removed. 3.4 Number of contacts 10 3.5 Annotation 10 2.2 Multiple sequence alignment for 2jguA 3.6 Mutation suggestions 11 For the chain 2jguA, the alignment 2jguA.msf (attached) with 79 sequences was used. The alignment was assembled through combi- 4 Appendix 11 nation of BLAST searching on the UniProt database and alignment 4.1 File formats 11 using Muscle program. It can be found in the attachment to this 4.2 Color schemes used 11 report, under the name of 2jguA.msf. Its statistics, from the alistat 4.3 Credits 11 program are the following: 1 Lichtarge lab 2006 Fig. 1. Residues 1-237 in 2jguA colored by their relative importance. (See Fig. 3. Residues 475-758 in 2jguA colored by their relative importance. (See Appendix, Fig.13, for the coloring scheme.) Appendix, Fig.13, for the coloring scheme.) 2.4 Top ranking residues in 2jguA and their position on the structure In the following we consider residues ranking among top 25% of resi- dues in the protein . Figure 4 shows residues in 2jguA colored by their importance: bright red and yellow indicate more conserved/important residues (see Appendix for the coloring scheme). A Pymol script for producing this figure can be found in the attachment. Fig. 2. Residues 238-474 in 2jguA colored by their relative importance. (See Appendix, Fig.13, for the coloring scheme.) Format: MSF Number of sequences: 79 Total number of residues: 53686 Smallest: 566 Largest: 712 Average length: 679.6 Alignment length: 712 Average identity: 29% Most related pair: 99% Most unrelated pair: 17% Most distant seq: 32% Furthermore, 1% of residues show as conserved in this alignment. The alignment consists of 31% eukaryotic ( 11% vertebrata, 11% Fig. 4. Residues in 2jguA, colored by their relative importance. Clockwise: fungi, 2% plantae), 12% prokaryotic, 39% archaean, and 17% viral front, back, top and bottom views. sequences. (Descriptions of some sequences were not readily availa- ble.) The file containing the sequence descriptions can be found in the attachment, under the name 2jguA.descr. 2.4.1 Clustering of residues at 25% coverage. Fig. 5 shows the top 25% of all residues, this time colored according to clusters they 2.3 Residue ranking in 2jguA belong to. The clusters in Fig.5 are composed of the residues listed The 2jguA sequence is shown in Figs. 1–3, with each residue colored in Table 1. according to its estimated importance. The full listing of residues in 2jguA can be found in the file called 2jguA.ranks sorted in the attachment. 2 Table 1. continued cluster size member color residues yellow 8 679,680,681,683,684,700,702 703 green 7 617,619,621,661,729,732,733 purple 5 19,203,204,254,255 azure 2 343,345 Table 1. Clusters of top ranking residues in 2jguA. 2.4.2 Overlap with known functional surfaces at 25% coverage. The name of the ligand is composed of the source PDB identifier and the heteroatom name used in that file. Manganese (ii) ion binding site. Table 2 lists the top 25% of resi- dues at the interface with 2jguAMN1758 (manganese (ii) ion). The following table (Table 3) suggests possible disruptive replacements for these residues (see Section 3.6). Table 2. res type subst’s cvg noc/ dist antn (%) bb (A˚ ) Fig. 5. Residues in 2jguA, colored according to the cluster they belong to: red, followed by blue and yellow are the largest clusters (see Appendix for 343 D D(26) 0.20 3/0 3.39 site the coloring scheme). Clockwise: front, back, top and bottom views. The Q(6) corresponding Pymol script is attached. C(5) E(7) Y(13) Table 1. R(34) cluster size member F(6) color residues red 120 37,39,111,113,114,119,123 Table 2. The top 25% of residues in 2jguA at the interface with manga- 329,332,348,349,350,352,353 nese (ii) ion.(Field names: res: residue number in the PDB entry; type: amino 356,357,361,368,369,385,387 acid type; substs: substitutions seen in the alignment; with the percentage of 388,390,393,396,397,398,401 each type in the bracket; noc/bb: number of contacts with the ligand, with 403,404,405,406,408,409,410 the number of contacts realized through backbone atoms given in the bracket; 411,412,413,414,418,419,420 dist: distance of closest apporach to the ligand. ) 421,422,423,448,450,454,457 458,461,465,480,481,482,483 484,485,486,487,488,490,491 Table 3. 492,493,494,495,496,497,498 res type disruptive 499,503,504,505,506,507,510 mutations 511,512,513,514,515,518,519 343 D (R)(FW)(H)(VA) 522,537,539,540,541,542,543 544,546,569,572,575,576,578 Table 3. List of disruptive mutations for the top 25% of residues in 2jguA, 579,581,582,584,587,588,589 that are at the interface with manganese (ii) ion. 590,591,592,593,594,595,596 597,607,608,609,610,632,744 Figure 6 shows residues in 2jguA colored by their importance, at the 745 interface with 2jguAMN1758. blue 33 140,141,142,143,144,187,191 Manganese (ii) ion binding site. Table 4 lists the top 25% of resi- 194,207,208,209,210,214,215 dues at the interface with 2jguAMN1759 (manganese (ii) ion). The 217,218,222,223,259,260,261 following table (Table 5) suggests possible disruptive replacements 270,273,275,278,283,287,308 for these residues (see Section 3.6). 311,315,316,319,322 Table 4. continued in next column res type subst’s cvg noc/ dist antn (%) bb (A˚ ) continued in next column 3 each type in the bracket; noc/bb: number of contacts with the ligand, with the number of contacts realized through backbone atoms given in the bracket; dist: distance of closest apporach to the ligand. ) Table 5. res type disruptive mutations 315 D (R)(FWH)(Y)(VCAG) 143 E (FWH)(Y)(R)(CG) 141 D (R)(H)(FW)(K) 311 Y (K)(EQ)(M)(R) 142 I (R)(Y)(H)(KE) Table 5. List of disruptive mutations for the top 25% of residues in 2jguA, that are at the interface with manganese (ii) ion. Fig. 6. Residues in 2jguA, at the interface with manganese (ii) ion, colored by their relative importance. The ligand (manganese (ii) ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well as on the line of sight to the ligand were removed. (See Appendix for the coloring scheme for the protein chain 2jguA.) Table 4. continued res type subst’s cvg noc/ dist antn (%) bb (A˚ ) 315 D D(98) 0.03 4/0 2.03 N(1) 143 E E(88) 0.05 4/0 2.14 site K(8) S(1) V(1) 141 D D(87) 0.10 4/0 2.23 site A(2) S(7) G(1) Fig. 7. Residues in 2jguA, at the interface with manganese (ii) ion, colored N(1) by their relative importance. The ligand (manganese (ii) ion) is colored green. Atoms further than 30A˚ away from the geometric center of the ligand, as well 311 Y Y(87) 0.10 3/0 4.22 as on the line of sight to the ligand were removed. (See Appendix for the H(8) coloring scheme for the protein chain 2jguA.) L(1) N(1) W(1) Figure 7 shows residues in 2jguA colored by their importance, at the 142 I I(84) 0.17 3/3 3.31 site interface with 2jguAMN1759.
Load more

Recommended publications
  • Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
    GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs.
    [Show full text]
  • TK1299, a Highly Thermostable NAD(P)H Oxidase from Thermococcus Kodakaraensis Exhibiting Higher Enzymatic Activity with NADPH
    TK1299, a highly thermostable NAD(P)H oxidase from Thermococcus kodakaraensis exhibiting higher enzymatic activity with NADPH Muhammad Atif Nisar,1 Naeem Rashid,1,* Qamar Bashir,1 Qurra-tul-Ann Afza Gardner,1 Muhammad Hassan Shafiq,1 and Muhammad Akhtar1,2 School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Punjab, Pakistan1 and School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK2 Received 27 November 2012; accepted 28 January 2013 Available online 26 February 2013 Seven nicotinamide adenine dinucleotide oxidase homologs have been found in the genome of Thermococcus koda- karaensis. The gene encoding one of them, TK1299, consisted of 1326 nucleotides, corresponding to a polypeptide of 442 amino acids. To examine the molecular properties of TK1299, the structural gene was cloned, expressed in Escherichia coli and the gene product was characterized. Molecular weight of the recombinant protein was 49,375 Da when determined by matrix-assisted laser desorption/ionization time-of-flight and 300 kDa when analyzed by gel filtration chromatography indicating that it existed in a hexameric form. The enzyme was highly thermostable even in boiling water where it exhibited more than 95% of the enzyme activity after incubation of 150 min. TK1299 catalyzed the oxidation of NADH as well as NADPH and predominantly converted O2 to H2O (more than 75%). Km value of the enzyme towards NADH and NADPH was almost same (24 ± 2 mM) where as specific activity was higher with NADPH compared to NADH. To our knowledge this is the most thermostable and unique NAD(P)H oxidase displaying higher enzyme activity with NADPH.
    [Show full text]
  • 1Pft Lichtarge Lab 2006
    Pages 1–6 1pft Evolutionary trace report by report maker August 6, 2010 4.3.1 Alistat 5 4.3.2 CE 5 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 5 4.5 Citing this work 5 4.6 About report maker 6 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1pft): Title: N-terminal domain of tfiib, nmr Compound: Mol id: 1; molecule: tfiib; chain: a; fragment: n- terminal domain; synonym: pftfiibn; engineered: yes Organism, scientific name: Pyrococcus Furiosus; 1pft contains a single unique chain 1pftA (50 residues long). This is an NMR-determined structure – in this report the first model in the file was used. CONTENTS 2 CHAIN 1PFTA 1 Introduction 1 2.1 P61999 overview 2 Chain 1pftA 1 From SwissProt, id P61999, 97% identical to 1pftA: 2.1 P61999 overview 1 Description: Transcription initiation factor IIB (TFIIB). 2.2 Multiple sequence alignment for 1pftA 1 Organism, scientific name: Pyrococcus woesei. 2.3 Residue ranking in 1pftA 1 Taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococca- 2.4 Top ranking residues in 1pftA and their position on les; Thermococcaceae; Pyrococcus. the structure 1 Function: Stabilizes TBP binding to an archaeal box-A promo- 2.4.1 Clustering of residues at 26% coverage. 2 ter. Also responsible for recruiting RNA polymerase II to the pre- 2.4.2 Overlap with known functional surfaces at initiation complex (DNA-TBP-TFIIB). 26% coverage.
    [Show full text]
  • Widespread Distribution of Archaeal Reverse Gyrase in Thermophilic Bacteria Suggests a Complex History of Vertical Inheritance and Lateral Gene Transfers
    Archaea 2, 83–93 © 2006 Heron Publishing—Victoria, Canada Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers CÉLINE BROCHIER-ARMANET1,3 and PATRICK FORTERRE2,4 1 EA 3781 EGEE (Evolution Génome Environnement), Université de Provence Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo 13331, Marseille Cedex 3, France 2 Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France 3 Corresponding author ([email protected]) 4 Unité Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France Received September 21, 2005; accepted May 26, 2006; published online August 18, 2006 Summary Reverse gyrase, an enzyme of uncertain funtion, Introduction is present in all hyperthermophilic archaea and bacteria. Previ- Reverse gyrase, an enzyme first discovered in the hyper- ous phylogenetic studies have suggested that the gene for re- thermophilic archaeon Sulfolobus acidocaldarius, is formed verse gyrase has an archaeal origin and was transferred later- by the combination of an N-terminal helicase module and a ally (LGT) to the ancestors of the two bacterial hyperther- C-terminal topoisomerase module (see Declais et al. 2000 for mophilic phyla, Thermotogales and Aquificales. Here, we per- a review). Comparative genomic analysis performed 4 years formed an in-depth analysis of the evolutionary history of ago showed that reverse gyrase was at that time the only pro- reverse gyrase in light of genomic progress. We found genes tein specific for hyperthermophiles (i.e., present in all hyper- coding for reverse gyrase in the genomes of several ther- thermophiles and absent in all non-hyperthermophiles) (For- mophilic bacteria that belong to phyla other than Aquificales and Thermotogales.
    [Show full text]
  • 1Iu9 Lichtarge Lab 2006
    Pages 1–5 1iu9 Evolutionary trace report by report maker July 1, 2010 4.3.3 DSSP 4 4.3.4 HSSP 4 4.3.5 LaTex 4 4.3.6 Muscle 4 4.3.7 Pymol 4 4.4 Note about ET Viewer 5 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 5 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1iu9): Title: Crystal structure of the c-terminal domain of aspartate race- mase from pyrococcus horikoshii ot3 Compound: Mol id: 1; molecule: aspartate racemase; chain: a; fragment: c-terminal domain; ec: 5.1.1.13; engineered: yes Organism, scientific name: Pyrococcus Horikoshii; 1iu9 contains a single unique chain 1iu9A (111 residues long). 2 CHAIN 1IU9A 2.1 O58403 overview CONTENTS From SwissProt, id O58403, 100% identical to 1iu9A: 1 Introduction 1 Description: 228aa long hypothetical aspartate racemase. Organism, scientific name: Pyrococcus horikoshii. 2 Chain 1iu9A 1 Taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococca- 2.1 O58403 overview 1 les; Thermococcaceae; Pyrococcus. 2.2 Multiple sequence alignment for 1iu9A 1 2.3 Residue ranking in 1iu9A 1 2.2 Multiple sequence alignment for 1iu9A 2.4 Top ranking residues in 1iu9A and their position on For the chain 1iu9A, the alignment 1iu9A.msf (attached) with 187 the structure 1 sequences was used. The alignment was downloaded from the HSSP 2.4.1 Clustering of residues at 25% coverage. 1 database, and fragments shorter than 75% of the query as well as 2.4.2 Possible novel functional surfaces at 25% duplicate sequences were removed.
    [Show full text]
  • University of Florida Thesis Or Dissertation Formatting
    CHARACTERIZING THE MOLECULAR MECHANISMS CONTRIBUTING TO BIOLOGICALLY INDUCED CARBONATE MINERALIZATION AND THROMBOLITE FORMATION By ARTEMIS S. LOUYAKIS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2017 © 2017 Artemis S. Louyakis To my mother, for supporting every single goal I’ve ever had, the memory of my father, for keeping me focused, and my partner, for all he’s done ACKNOWLEDGMENTS I would like to begin by acknowledging and thanking my mentor, Dr. Jamie Foster, for all her guidance throughout this Ph.D. I thank my committee members for all of their advice and support - Drs. Eric Triplett, Julie Maupin, Nian Wang, and Eric McLamore. I’d like to thank the rest of the Department of Microbiology and Cell Science, staff for always keeping my academic life in order, faculty for never turning me away when I came to use equipment or ask for help, especially Drs. K.T. Shanmugan and Wayne Nicholson, as well as Dr. Andy Schuerger from the Dept. of Plant Pathology for his advice over the years. I’d also like to acknowledge those lab members and extended lab members who made themselves readily available to talk through any problems I came up against and celebrate when all went well, including Drs. Rafael Oliveira, Jennifer Mobberley, and Giorgio Casaburi, and Lexi Duscher, Rachelle Banjawo, Maddie Vroom, Hadrien Gourlé, and so many more. I’d also like to profusely thank my family and friends who have never been anything less than completely supportive of me, specifically my partner Nathan Prince, my mother and siblings Denise Louyakis, Bobbi Louyakis, Nick Newman, Cori Sergi, extended parents and siblings Carol Prince, Barry Prince, Aaron Prince, my nieces and nephew Bailey O’Regan, Bella O’Regan, Layla Newman, Colton Prince, and Summer Prince, and my dearest friends Tina Pontbriand, Tom Pontbriand, Karen Chan, Dalal Haouchar, Alexi Casaburi, and Eloise Stikeman.
    [Show full text]
  • Identification and Characterization of a New Transcription Factor
    IDENTIFICATION AND CHARACTERIZATION OF A NEW TRANSCRIPTION FACTOR INVOLVED IN PYROCOCCUS FURIOSUS RESPONSE TO OXIDATIVE STRESS by SUNGGUAN HONG (Under the Direction of Robert A. Scott) ABSTRACT Gene expression is often under regulation at the transcriptional level, controlled by transcription factors. The primary goal of this research project is to discover and characterize new transcription factors in Pyrococcus furiosus (Pf), a model archaeal organism. The transcription system of archaea has both bacterial-like and eukaryotic-like features. Only a very limited number of archaeal transcription regulatory proteins have been identified to date, and transcription regulatory pathways are far from being well known. In this project, transcription factors were discovered using DNA affinity protein capture followed by mass spectrometry based protein identification. The Pf gene expression profile on the genome-wide scale has been described and compared between two different cell-growth conditions with cumene hydroperoxide and without cumene hydroperoxide. Additional bioinformatics analysis identified a conserved palindromic sequence in the putative promoter region of several genes that are upregulated by growth with cumene hydroperoxide and all are involved in oxidative stress. Based on these analyses, the DNA fragments upstream of the open reading frame of PF1983 and PF1513, which both encode hypothetical protein, were selected for DNA-affinity protein capture. A novel transcription regulatory protein PF0230p was identified and its specific DNA binding ability at sites upstream of multiple genes was confirmed by the electrophoretic mobility shift assay (EMSA). DNase I footprinting showed that PF0230p binds to a region upstream of both PF1983 and PF1513, which contains the conserved palindromic motif, ATTAAT.
    [Show full text]
  • Supplementary Material For: Undinarchaeota Illuminate The
    Supplementary Material for: Undinarchaeota illuminate the evolution of DPANN archaea Nina Dombrowski1, Tom A. Williams2, Benjamin J. Woodcroft3, Jiarui Sun3, Jun-Hoe Lee4, Bui Quang MinH5, CHristian Rinke5, Anja Spang1,5,# 1NIOZ, Royal NetHerlands Institute for Sea ResearcH, Department of Marine Microbiology and BiogeocHemistry, and UtrecHt University, P.O. Box 59, NL-1790 AB Den Burg, THe NetHerlands 2 ScHool of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK 3Australian Centre for Ecogenomics, ScHool of CHemistry and Molecular Biosciences, THe University of Queensland, QLD 4072, Australia 4Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden 5ResearcH ScHool of Computer Science and ResearcH ScHool of Biology, Australian National University, ACT 2601, Australia #corresponding autHor. Postal address: Landsdiep 4, 1797 SZ 't Horntje (Texel). Email address: [email protected]. PHone number: +31 (0)222 369 526 Table of Contents Table of Contents 2 General 3 Evaluating CHeckM completeness estimates 3 Screening for contaminants 3 Phylogenetic analyses 4 Informational processing and repair systems 7 Replication and cell division 7 Transcription 7 Translation 8 DNA-repair and modification 9 Stress tolerance 9 Metabolic features 10 Central carbon and energy metabolism 10 Anabolism 13 Purine and pyrimidine biosyntHesis 13 Amino acid degradation and biosyntHesis 14 Lipid biosyntHesis 15 Vitamin and cofactor biosyntHesis 16 Host-symbiont interactions 16 Genes potentially
    [Show full text]
  • 1S04 Lichtarge Lab 2006
    Pages 1–6 1s04 Evolutionary trace report by report maker June 12, 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 5 4.5 Citing this work 5 4.6 About report maker 5 4.7 Attachments 6 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 1s04): Title: Solution nmr structure of protein pf0455 from pyrococcus furiosus. northeast structural genomics consortium target pfr13 Compound: Mol id: 1; molecule: hypothetical protein pf0455; chain: a; engineered: yes CONTENTS Organism, scientific name: Pyrococcus Furiosus; 1s04 contains a single unique chain 1s04A (110 residues long). 1 Introduction 1 This is an NMR-determined structure – in this report the first model 2 Chain 1s04A 1 in the file was used. 2.1 Q8U3L1 overview 1 2.2 Multiple sequence alignment for 1s04A 1 2.3 Residue ranking in 1s04A 1 2.4 Top ranking residues in 1s04A and their position on the structure 1 2.4.1 Clustering of residues at 25% coverage. 1 2 CHAIN 1S04A 2.4.2 Possible novel functional surfaces at 25% 2.1 Q8U3L1 overview coverage. 2 From SwissProt, id Q8U3L1, 83% identical to 1s04A: Description: Hypothetical protein PF0455. 3 Notes on using trace results 4 Organism, scientific name: Pyrococcus furiosus. 3.1 Coverage 4 Taxonomy: Archaea; Euryarchaeota; Thermococci; Thermococca- 3.2 Known substitutions 4 les; Thermococcaceae; Pyrococcus. 3.3 Surface 4 3.4 Number of contacts 4 3.5 Annotation 4 3.6 Mutation suggestions 4 2.2 Multiple sequence alignment for 1s04A 4 Appendix 4 For the chain 1s04A, the alignment 1s04A.msf (attached) with 30 4.1 File formats 4 sequences was used.
    [Show full text]
  • Flexibility in the Mineral Dependent Metabolism of A
    FLEXIBILITY IN THE MINERAL DEPENDENT METABOLISM OF A THERMOACIDOPHILIC CRENARCHAEOTE by Maximiliano Jose Amenabar Barriuso A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology MONTANA STATE UNIVERSITY Bozeman, Montana August 2017 ©COPYRIGHT by Maximiliano Jose Amenabar Barriuso 2017 All Rights Reserved ii DEDICATION For my wife Ivonne who has been the pillar of support and love in my life and for my daughters Martina and Trinidad who are the ones that inspire my life every day. iii ACKNOWLEDGEMENTS I would like to extend my gratitude to Dr. Eric Boyd for all his time and patience in guiding me through all my Ph.D. It is hard to express my gratitude to him in just a few words, but I just could say that I have been really lucky to learn from him. I also would like to express my thanks to Dr. John Peters for giving me the opportunity to join his lab and making my life easier in applying and attending Montana State University. I am also thankful to everyone in the Boyd lab: Dan, John, Melody, Saroj, Eric D., Erik A., Libby and former lab member Matt Urschel for being such a fun and smart group of people to work with. Thanks also to the various co-authors who contributed to the chapters of these dissertation and to my committee members: Dr. Matthew Fields, Dr. Mark Skidmore and Dr. John Peters; all of you helped me grow as a scientist. I am also thankful to the Department of Microbiology and Immunology for believing in me and giving me the opportunity to join the Department to do my PhD, and also to all the former and current staff from the Department for helping me any time I need it.
    [Show full text]
  • Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales Alhr2 DNA/RNA Helicase
    biomolecules Article Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase Mirna Hajj 1,2,† , Petra Langendijk-Genevaux 1,† , Manon Batista 1, Yves Quentin 1,Sébastien Laurent 3, Régine Capeyrou 4, Ziad Abdel-Razzak 2, Didier Flament 3, Hala Chamieh 2, Gwennaele Fichant 1,*, Béatrice Clouet-d’Orval 1,4,* and Marie Bouvier 1,4 1 Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France; [email protected] (M.H.); [email protected] (P.L.-G.); [email protected] (M.B.); [email protected] (Y.Q.); [email protected] (M.B.) 2 Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Application, EDST, Lebanese University, Tripoli 1300, Lebanon; [email protected] (Z.A.-R.); [email protected] (H.C.) 3 Ifremer, Univ Brest, CNRS, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France; [email protected] (S.L.); [email protected] (D.F.) 4 Laboratoire de Biologie Moléculaire, Cellulaire et du Développement, UMR5077, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, F-31062 Toulouse, France; [email protected] * Correspondence: gwennaele.fi[email protected] (G.F.); [email protected] (B.C.-d.) † Co-first authors. Citation: Hajj, M.; Langendijk-Genevaux, P.; Batista, M.; Abstract: Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to Quentin, Y.; Laurent, S.; Capeyrou, R.; remodel protein-nucleic acid complexes.
    [Show full text]
  • Specific Enrichment of Hyperthermophilic Electroactive Archaea from Deep-Sea Hydrothermal Vent on Electrically Conductive Support
    1 Bioresource Technology Archimer July 2018, Volume 259, Pages 304-311 http://dx.doi.org/10.1016/j.biortech.2018.03.053 http://archimer.ifremer.fr http://archimer.ifremer.fr/doc/00431/54228/ © 2018 Elsevier Ltd. All rights reserved. Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support. Pillot Guillaume 1, Frouin Eléonore 1, Pasero Emilie 1, Godfroy Anne 2, Combet-Blanc Yannick 1, Davidson Sylvain 1, Liebgott Pierre-Pol 1, * 1 Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France. 2 IFREMER, CNRS, Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes - UMR6197, Ifremer, Centre de Brest CS10070, Plouzané, France. * Corresponding author : Pierre-Pol Liebgott, email address : [email protected] Abstract : While more and more investigations are done to study hyperthermophilic exoelectrogenic communities from environments, none have been performed yet on deep-sea hydrothermal vent. Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic (80 °C) condition. Two enrichments were performed in a BioElectrochemical System specially designed: one from direct inoculation of crushed chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both experiments, a current production was observed from 2.4 A/m2 to 5.8 A/m2 with a set anode potential of -0.110 V vs Ag/AgCl. Taxonomic affiliation of the exoelectrogen communities obtained on the electrode exhibited a specific enrichment of Archaea belonging to Thermococcales and Archeoglobales orders, even when both inocula were dominated by Bacteria.
    [Show full text]