Literature DB >> 20054114

The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603).

Richard W Strange1, Svetlana V Antonyuk, Mark J Ellis, Yoshitaka Bessho, Seiki Kuramitsu, Shigeyuki Yokoyama, S Samar Hasnain.   

Abstract

Ribose-5-phosphate isomerase is a ubiquitous intracellular enzyme of bacterial, plant and animal origin that is involved in the pentose phosphate cycle, an essential component of cellular carbohydrate metabolism. Specifically, the enzyme catalyses the reversible conversion of ribose 5-phosphate to ribulose 5-phosphate. The structure of ribose-5-phosphate isomerase from Methanocaldococcus jannaschii has been solved in space group P2(1) to 1.78 A resolution using molecular replacement with one homotetramer in the asymmetric unit and refined to an R factor of 14.8%. The active site in each subunit was occupied by two molecules of propylene glycol in different orientations, one of which corresponds to the location of the phosphate moiety and the other to the location of the furanose ring of the inhibitor.

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Year:  2009        PMID: 20054114      PMCID: PMC2802866          DOI: 10.1107/S1744309109044923

Source DB:  PubMed          Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun        ISSN: 1744-3091


  15 in total

1.  Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles.

Authors:  M K Essenberg; R A Cooper
Journal:  Eur J Biochem       Date:  1975-07-01

2.  Automated protein model building combined with iterative structure refinement.

Authors:  A Perrakis; R Morris; V S Lamzin
Journal:  Nat Struct Biol       Date:  1999-05

3.  A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii characterization and three-dimensional structure.

Authors:  Kazuhiko Ishikawa; Ikuo Matsui; Francoise Payan; Christian Cambillau; Hiroyasu Ishida; Yutaka Kawarabayasi; Hisasi Kikuchi; Alain Roussel
Journal:  Structure       Date:  2002-06       Impact factor: 5.006

4.  Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli.

Authors:  Erumbi S Rangarajan; J Sivaraman; Allan Matte; Miroslaw Cygler
Journal:  Proteins       Date:  2002-09-01

5.  Refinement of macromolecular structures by the maximum-likelihood method.

Authors:  G N Murshudov; A A Vagin; E J Dodson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1997-05-01

6.  High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center.

Authors:  Michihiro Sugahara; Yukuhiko Asada; Katsumi Shimizu; Hitoshi Yamamoto; Neratur K Lokanath; Hisashi Mizutani; Bagautdin Bagautdinov; Yoshinori Matsuura; Midori Taketa; Yuichi Kageyama; Naoko Ono; Yuko Morikawa; Yukiko Tanaka; Hiroki Shimada; Takanobu Nakamoto; Mitsuaki Sugahara; Masaki Yamamoto; Naoki Kunishima
Journal:  J Struct Funct Genomics       Date:  2008-08-02

7.  Structure of ribose 5-phosphate isomerase from Plasmodium falciparum.

Authors:  Margaret A Holmes; Frederick S Buckner; Wesley C Van Voorhis; Christophe L M J Verlinde; Christopher Mehlin; Erica Boni; George DeTitta; Joseph Luft; Angela Lauricella; Lori Anderson; Oleksandr Kalyuzhniy; Frank Zucker; Lori W Schoenfeld; Thomas N Earnest; Wim G J Hol; Ethan A Merritt
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2006-04-12

8.  D-ribose-5-phosphate isomerase from spinach: heterologous overexpression, purification, characterization, and site-directed mutagenesis of the recombinant enzyme.

Authors:  C H Jung; F C Hartman; T Y Lu; F W Larimer
Journal:  Arch Biochem Biophys       Date:  2000-01-15       Impact factor: 4.013

9.  Regulation of ribose metabolism in Escherichia coli. II. Evidence for two ribose-5-phosphate isomerase activities.

Authors:  J David; H Wiesmeyer
Journal:  Biochim Biophys Acta       Date:  1970-04-14

10.  MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

Authors:  Ian W Davis; Andrew Leaver-Fay; Vincent B Chen; Jeremy N Block; Gary J Kapral; Xueyi Wang; Laura W Murray; W Bryan Arendall; Jack Snoeyink; Jane S Richardson; David C Richardson
Journal:  Nucleic Acids Res       Date:  2007-04-22       Impact factor: 16.971

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  3 in total

1.  Structure of ribose 5-phosphate isomerase from the probiotic bacterium Lactobacillus salivarius UCC118.

Authors:  Carina M C Lobley; Pierre Aller; Alice Douangamath; Yamini Reddivari; Mario Bumann; Louise E Bird; Joanne E Nettleship; Jose Brandao-Neto; Raymond J Owens; Paul W O'Toole; Martin A Walsh
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-11-14

Review 2.  Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation.

Authors:  Christopher Bräsen; Dominik Esser; Bernadette Rauch; Bettina Siebers
Journal:  Microbiol Mol Biol Rev       Date:  2014-03       Impact factor: 11.056

3.  Concerted proton transfer mechanism of Clostridium thermocellum ribose-5-phosphate isomerase.

Authors:  Jun Wang; Weitao Yang
Journal:  J Phys Chem B       Date:  2013-08-02       Impact factor: 2.991

  3 in total

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