2yx0
From Proteopedia
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| - | [[Image:2yx0.gif|left|200px]] | + | [[Image:2yx0.gif|left|200px]] |
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| - | '''Crystal structure of P. horikoshii TYW1''' | + | {{Structure |
| + | |PDB= 2yx0 |SIZE=350|CAPTION= <scene name='initialview01'>2yx0</scene>, resolution 2.21Å | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
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| + | '''Crystal structure of P. horikoshii TYW1''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2YX0 is a [ | + | 2YX0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX0 OCA]. |
==Reference== | ==Reference== | ||
| - | Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis., Goto-Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine SI, Bessho Y, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1059-68. Epub 2007, Sep 19. PMID:[http:// | + | Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis., Goto-Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine SI, Bessho Y, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1059-68. Epub 2007, Sep 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17881823 17881823] |
[[Category: Pyrococcus horikoshii]] | [[Category: Pyrococcus horikoshii]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
[[Category: metal binding protein]] | [[Category: metal binding protein]] | ||
| - | [[Category: national project on protein structural and functional | + | [[Category: national project on protein structural and functional analyse]] |
[[Category: nppsfa]] | [[Category: nppsfa]] | ||
[[Category: predicted trna modification enzyme]] | [[Category: predicted trna modification enzyme]] | ||
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[[Category: riken structural genomics/proteomics initiative]] | [[Category: riken structural genomics/proteomics initiative]] | ||
[[Category: rsgi]] | [[Category: rsgi]] | ||
| - | [[Category: structural | + | [[Category: structural genomic]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:50:00 2008'' |
Revision as of 16:50, 20 March 2008
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| , resolution 2.21Å | |||||||
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of P. horikoshii TYW1
Overview
Wye bases are tricyclic bases that are found in archaeal and eukaryotic tRNAs. The most modified wye base, wybutosine, which appears at position 37 (the 3'-adjacent position to the anticodon), is known to be important for translational reading-frame maintenance. Saccharomyces cerevisiae TYW1 catalyzes the tri-ring-formation step in wye-base biosynthesis, with the substrate tRNA bearing N(1)-methylated G37. Here, the crystal structure of the archaeal TYW1 homologue from Pyrococcus horikoshii is reported at 2.2 A resolution. The amino-acid sequence of P. horikoshii TYW1 suggested that it is a radical-AdoMet enzyme and the tertiary structure of P. horikoshii TYW1 indeed shares the modified TIM-barrel structure found in other radical-AdoMet enzymes. Radical-AdoMet enzymes generally contain one or two iron-sulfur (FeS) clusters. The tertiary structure of P. horikoshii TYW1 revealed two FeS cluster sites, each containing three cysteine residues. One FeS cluster site was expected from the amino-acid sequence and the other involves cysteine residues that are dispersed throughout the sequence. The existence of two FeS clusters was confirmed from the anomalous Fourier electron-density map. By superposing the P. horikoshii TYW1 tertiary structure on those of other radical-AdoMet enzymes, the AdoMet molecule, which is necessary for the reactions of radical-AdoMet enzymes, was modelled in P. horikoshii TYW1. Surface plots of conservation rates and electrostatic potentials revealed the highly conserved and positively charged active-site hollow. On the basis of the surface properties, a docking model of P. horikoshii TYW1, the tRNA, the FeS clusters and the AdoMet molecule was constructed, with the nucleoside at position 37 of tRNA flipped out from the canonical tRNA structure.
About this Structure
2YX0 is a Single protein structure of sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA.
Reference
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis., Goto-Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine SI, Bessho Y, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1059-68. Epub 2007, Sep 19. PMID:17881823
Page seeded by OCA on Thu Mar 20 18:50:00 2008
Categories: Pyrococcus horikoshii | Single protein | Bessho, Y. | Fusatomi, E. | Goto-Ito, S. | Ishii, R. | Ito, T. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Sekine, S. | Shibata, R. | Yokoyama, S. | Metal binding protein | National project on protein structural and functional analyse | Nppsfa | Predicted trna modification enzyme | Radical sam enzyme | Riken structural genomics/proteomics initiative | Rsgi | Structural genomic
