Literature DB >> 20053843

dbTEU: a protein database of trace element utilization.

Yan Zhang1, Vadim N Gladyshev.   

Abstract

UNLABELLED: Biological trace elements are required for numerous biological processes and by all organisms. We describe a database, dbTEU (DataBase of Trace Element Utilization), that features known transporters and user proteins for five trace elements (copper, molybdenum, nickel, cobalt and selenium) and represents sequenced organisms from the three domains of life. The manually curated dbTEU currently includes approximately 16,500 proteins from >700 organisms, and offers interactive trace element, protein, organism and sequence search and browse tools.
AVAILABILITY AND IMPLEMENTATION: dbTEU is freely available at http://gladyshevlab.bwh.harvard.edu/trace_element/

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Year:  2010        PMID： 20053843      PMCID： PMC2828109          DOI： 10.1093/bioinformatics/btp705

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  16 in total

1.  The prokaryotic selenoproteome.

Authors:  Gregory V Kryukov; Vadim N Gladyshev
Journal:  EMBO Rep       Date:  2004-04-23       Impact factor: 8.807

2.  An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes.

Authors:  Yan Zhang; Vadim N Gladyshev
Journal:  Bioinformatics       Date:  2005-03-29       Impact factor: 6.937

3.  Zinc through the three domains of life.

Authors:  Claudia Andreini; Lucia Banci; Ivano Bertini; Antonio Rosato
Journal:  J Proteome Res       Date:  2006-11       Impact factor: 4.466

4.  Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry.

Authors:  Christopher L Dupont; Song Yang; Brian Palenik; Philip E Bourne
Journal:  Proc Natl Acad Sci U S A       Date:  2006-11-10       Impact factor: 11.205

5.  New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements.

Authors:  G V Kryukov; V M Kryukov; V N Gladyshev
Journal:  J Biol Chem       Date:  1999-11-26       Impact factor: 5.157

6.  Characterization of mammalian selenoproteomes.

Authors:  Gregory V Kryukov; Sergi Castellano; Sergey V Novoselov; Alexey V Lobanov; Omid Zehtab; Roderic Guigó; Vadim N Gladyshev
Journal:  Science       Date:  2003-05-30       Impact factor: 47.728

Review 7.  Eukaryotic selenoproteins and selenoproteomes.

Authors:  Alexey V Lobanov; Dolph L Hatfield; Vadim N Gladyshev
Journal:  Biochim Biophys Acta       Date:  2009-05-27

Review 8.  Selenocysteine: the 21st amino acid.

Authors:  A Böck; K Forchhammer; J Heider; W Leinfelder; G Sawers; B Veprek; F Zinoni
Journal:  Mol Microbiol       Date:  1991-03       Impact factor: 3.501

Review 9.  Metal and cofactor insertion.

Authors:  Ralf R Mendel; Alison G Smith; Andree Marquet; Martin J Warren
Journal:  Nat Prod Rep       Date:  2007-09-12       Impact factor: 13.423

10.  Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen.

Authors:  Perry G Ridge; Yan Zhang; Vadim N Gladyshev
Journal:  PLoS One       Date:  2008-01-02       Impact factor: 3.240
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  9 in total

Review 1.  Redox biology: computational approaches to the investigation of functional cysteine residues.

Authors:  Stefano M Marino; Vadim N Gladyshev
Journal:  Antioxid Redox Signal       Date:  2011-04-14       Impact factor: 8.401

2.  Selenium-dependent biogenesis of formate dehydrogenase in Campylobacter jejuni is controlled by the fdhTU accessory genes.

Authors:  Frances L Shaw; Francis Mulholland; Gwénaëlle Le Gall; Ida Porcelli; Dave J Hart; Bruce M Pearson; Arnoud H M van Vliet
Journal:  J Bacteriol       Date:  2012-05-18       Impact factor: 3.490

3.  Bioinformatics of Selenoproteins.

Authors:  Didac Santesmasses; Marco Mariotti; Vadim N Gladyshev
Journal:  Antioxid Redox Signal       Date:  2020-04-23       Impact factor: 8.401

Review 4.  Bioinformatics of Metalloproteins and Metalloproteomes.

Authors:  Yan Zhang; Junge Zheng
Journal:  Molecules       Date:  2020-07-24       Impact factor: 4.411

5.  InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information.

Authors:  Józef Ba Tran; Artur Krężel
Journal:  J Proteome Res       Date:  2021-01-27       Impact factor: 4.466

6.  Macrophage Selenoproteins Restrict Intracellular Replication of Francisella tularensis and Are Essential for Host Immunity.

Authors:  Rachel L Markley; Katherine H Restori; Bhuvana Katkere; Sarah E Sumner; McKayla J Nicol; Anastasia Tyryshkina; Shaneice K Nettleford; David R Williamson; David E Place; Kalyan K Dewan; Ashley E Shay; Bradley A Carlson; Santhosh Girirajan; K Sandeep Prabhu; Girish S Kirimanjeswara
Journal:  Front Immunol       Date:  2021-10-29       Impact factor: 8.786

7.  Evolution of the Selenoproteome in Helicobacter pylori and Epsilonproteobacteria.

Authors:  Pietro Cravedi; Giulia Mori; Frédéric Fischer; Riccardo Percudani
Journal:  Genome Biol Evol       Date:  2015-09-04       Impact factor: 3.416

8.  Comparative genomics reveals new evolutionary and ecological patterns of selenium utilization in bacteria.

Authors:  Ting Peng; Jie Lin; Yin-Zhen Xu; Yan Zhang
Journal:  ISME J       Date:  2016-01-22       Impact factor: 10.302

Review 9.  The Mechanism of Metal Homeostasis in Plants: A New View on the Synergistic Regulation Pathway of Membrane Proteins, Lipids and Metal Ions.

Authors:  Danxia Wu; Muhammad Saleem; Tengbing He; Guandi He
Journal:  Membranes (Basel)       Date:  2021-12-15
  9 in total

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