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Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp 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. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000685155Cyc: Candidatus Methanoperedens nitroreducens ANME-2d Cellular Overview Connections between pathways are omitted for legibility.

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Molybdoproteomes and Evolution of Molybdenum Utilization
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Vadim Gladyshev Publications Biochemistry, Department of April 2008 Molybdoproteomes and evolution of molybdenum utilization Yan Zhang University of Nebraska-Lincoln, [email protected] Vadim N. Gladyshev University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biochemgladyshev Part of the Biochemistry, Biophysics, and Structural Biology Commons Zhang, Yan and Gladyshev, Vadim N., "Molybdoproteomes and evolution of molybdenum utilization" (2008). Vadim Gladyshev Publications. 78. https://digitalcommons.unl.edu/biochemgladyshev/78 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Vadim Gladyshev Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Journal of Molecular Biology (2008); doi: 10.1016/j.jmb.2008.03.051 Copyright © 2008 Elsevier. Used by permission. http://www.sciencedirect.com/science/journal/00222836 Submitted November 26, 2007; revised March 15, 2008; accepted March 25, 2008; published online as “Accepted Manuscript” April 1, 2008. Molybdoproteomes and evolution of molybdenum utilization Yan Zhang and Vadim N. Gladyshev* Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE 685880664 *Corresponding author—tel 402 472-4948, fax 402 472-7842, email [email protected] Abstract The trace element molybdenum (Mo) is utilized in many life forms, where it is a key component of several enzymes involved in nitrogen, sulfur, and carbon metabolism. With the exception of nitrogenase, Mo is bound in proteins to a pterin, thus forming the molybdenum cofactor (Moco) at the catalytic sites of molybdoenzymes.
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Articles Catalytic Cycling in Β-Phosphoglucomutase: a Kinetic
9404 Biochemistry 2005, 44, 9404-9416 Articles Catalytic Cycling in â-Phosphoglucomutase: A Kinetic and Structural Analysis†,‡ Guofeng Zhang, Jianying Dai, Liangbing Wang, and Debra Dunaway-Mariano* Department of Chemistry, UniVersity of New Mexico, Albuquerque, New Mexico 87131-0001 Lee W. Tremblay and Karen N. Allen* Department of Physiology and Biophysics, Boston UniVersity School of Medicine, Boston, Massachusetts 02118-2394 ReceiVed March 26, 2005; ReVised Manuscript ReceiVed May 18, 2005 ABSTRACT: Lactococcus lactis â-phosphoglucomutase (â-PGM) catalyzes the interconversion of â-D-glucose 1-phosphate (â-G1P) and â-D-glucose 6-phosphate (G6P), forming â-D-glucose 1,6-(bis)phosphate (â- G16P) as an intermediate. â-PGM conserves the core domain catalytic scaffold of the phosphatase branch of the HAD (haloalkanoic acid dehalogenase) enzyme superfamily, yet it has evolved to function as a mutase rather than as a phosphatase. This work was carried out to identify the structural basis underlying this diversification of function. In this paper, we examine â-PGM activation by the Mg2+ cofactor, â-PGM activation by Asp8 phosphorylation, and the role of cap domain closure in substrate discrimination. First, the 1.90 Å resolution X-ray crystal structure of the Mg2+-â-PGM complex is examined in the context of + + previously reported structures of the Mg2 -R-D-galactose-1-phosphate-â-PGM, Mg2 -phospho-â-PGM, and Mg2+-â-glucose-6-phosphate-1-phosphorane-â-PGM complexes to identify conformational changes that occur during catalytic turnover. The essential role of Asp8 in nucleophilic catalysis was confirmed by demonstrating that the D8A and D8E mutants are devoid of catalytic activity.
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Insights Into Diphthamide, Key Diphtheria Toxin Effector
Toxins 2013, 5, 958-968; doi:10.3390/toxins5050958 OPEN ACCESS toxins ISSN 2072-6651 www.mdpi.com/journal/toxins Brief Report Insights into Diphthamide, Key Diphtheria Toxin Effector Wael Abdel-Fattah 1,†, Viktor Scheidt 1,†, Shanow Uthman 2, Michael J. R. Stark 3 and Raffael Schaffrath 1,2,* 1 Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel D-34132, Germany; E-Mails: [email protected] (W.A.-F.); [email protected] (V.S.) 2 Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; E-Mail: [email protected] 3 Centre for Gene Regulation & Expression, University of Dundee, Dundee, DD1 5EH, Scotland; E-Mail: [email protected] † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-561-804-4175; Fax: +49-561-804-4337. Received: 14 March 2013; in revised form: 17 April 2013 / Accepted: 26 April 2013 / Published: 3 May 2013 Abstract: Diphtheria toxin (DT) inhibits eukaryotic translation elongation factor 2 (eEF2) by ADP-ribosylation in a fashion that requires diphthamide, a modified histidine residue on eEF2. In budding yeast, diphthamide formation involves seven genes, DPH1-DPH7. In an effort to further study diphthamide synthesis and interrelation among the Dph proteins, we found, by expression in E. coli and co-immune precipitation in yeast, that Dph1 and Dph2 interact and that they form a complex with Dph3. Protein-protein interaction mapping shows that Dph1-Dph3 complex formation can be dissected by progressive DPH1 gene truncations. This identifies N- and C-terminal domains on Dph1 that are crucial for diphthamide synthesis, DT action and cytotoxicity of sordarin, another microbial eEF2 inhibitor.
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Molybdenum Cofactor and Sulfite Oxidase Deficiency Jochen Reiss* Institute of Human Genetics, University Medicine Göttingen, Germany
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Expression of a Phosphoglucomutase Gene in Rainbow Trout (Polymorphism/Developmental Rate/Glycolysis/Salmo Gairdneri) FRED W
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Shared Sulfur Mobilization Routes for Trna Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes
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Protein-Protein Interactions of Human Mitochondrial Amidoxime-Reducing Component in Mammalian Cells John Thomas
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TABLE S3 Clusters of Gene Ontology Groups and Their Associated Genes
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And Ubiquitin-Like Proteins Provide a Direct Link Between Protein Conjugation and Sulfur Transfer in Archaea
E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea Hugo V. Mirandaa, Nikita Nembharda, Dan Sub, Nathaniel Hepowita, David J. Krausea, Jonathan R. Pritza, Cortlin Phillipsa, Dieter Söllb,c, and Julie A. Maupin-Furlowa,1 aDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700; and bDepartment of Molecular Biophysics and Biochemistry, and cDepartment of Chemistry, Yale University, New Haven, CT 06511 Edited* by Lonnie O’Neal Ingram, University of Florida, Gainesville, FL, and approved February 10, 2011 (received for review December 8, 2010) Based on our recent work with Haloferax volcanii, ubiquitin-like of tRNA synthetases are required for RNA-protein interactions, (iii) (Ubl) proteins (SAMP1 and SAMP2) are known to be covalently at- ThiS/MoaD proteins serve as sulfur carriers in thiamine and tung- tached to proteins in archaea. Here, we investigated the enzymes sten/molybdenum cofactor (W/MoCo) biosynthesis, and (iv)Atg8 required for the formation of these Ubl-protein conjugates (SAM- and LC3 are conjugated to phospholipids (5–8). Pylation) and whether this system is linked to sulfur transfer. Mar- β-Grasp fold-proteins that function as sulfur carriers and pro- kerless in-frame deletions were generated in H. volcanii target tein modiﬁers share a common chemistry. Both types of proteins i genes. The mutants were examined for: ( ) the formation of Ubl are adenylated at their C terminus by an ATP-dependent E1/ ii protein conjugates, ( ) growth under various conditions, including MoeB/ThiF-type enzyme (8, 9). This adenylation activates the those requiring the synthesis of the sulfur-containing molybdenum β-grasp fold-protein for either the acceptance of sulfur as a C- cofactor (MoCo), and (iii) the thiolation of tRNA.
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Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.
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Characterisation, Classification and Conformational Variability Of
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