1wyd: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1wyd.gif|left|200px]] | [[Image:1wyd.gif|left|200px]] | ||
'''Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii''' | {{Structure | ||
|PDB= 1wyd |SIZE=350|CAPTION= <scene name='initialview01'>1wyd</scene>, resolution 2.30Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID'>EPE</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
1WYD is a [ | 1WYD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_tokodaii Sulfolobus tokodaii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYD OCA]. | ||
==Reference== | ==Reference== | ||
Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons., Sato Y, Maeda Y, Shimizu S, Hossain MT, Ubukata S, Suzuki K, Sekiguchi T, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1042-7. Epub 2007, Sep 19. PMID:[http:// | Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons., Sato Y, Maeda Y, Shimizu S, Hossain MT, Ubukata S, Suzuki K, Sekiguchi T, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1042-7. Epub 2007, Sep 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17881821 17881821] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Sulfolobus tokodaii]] | [[Category: Sulfolobus tokodaii]] | ||
| Line 27: | Line 36: | ||
[[Category: sulfolobus tokodaii]] | [[Category: sulfolobus tokodaii]] | ||
''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 15:03:07 2008'' | ||
Revision as of 13:03, 20 March 2008
| |||||||||||||
| 1wyd, resolution 2.30Å | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ligands: | CL, SO4 and EPE | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii
Overview
In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNA(Asn) in addition to Asp-tRNA(Asp). In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St-AspRS (nondiscriminating type) has been determined at 2.3 A resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer.
About this Structure
1WYD is a Single protein structure of sequence from Sulfolobus tokodaii. Full crystallographic information is available from OCA.
Reference
Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons., Sato Y, Maeda Y, Shimizu S, Hossain MT, Ubukata S, Suzuki K, Sekiguchi T, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1042-7. Epub 2007, Sep 19. PMID:17881821
Page seeded by OCA on Thu Mar 20 15:03:07 2008
