1x8x: Difference between revisions
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[[Image:1x8x.gif|left|200px]] | [[Image:1x8x.gif|left|200px]] | ||
'''Tyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine''' | {{Structure | ||
|PDB= 1x8x |SIZE=350|CAPTION= <scene name='initialview01'>1x8x</scene>, resolution 2.00Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=TYR:TYROSINE'>TYR</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] | |||
|GENE= | |||
}} | |||
'''Tyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1X8X is a [ | 1X8X is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X8X OCA]. | ||
==Reference== | ==Reference== | ||
Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase., Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S, J Mol Biol. 2005 Feb 11;346(1):105-17. Epub 2004 Dec 15. PMID:[http:// | Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase., Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S, J Mol Biol. 2005 Feb 11;346(1):105-17. Epub 2004 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15663931 15663931] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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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 15:06:36 2008'' | ||
Revision as of 16:06, 20 March 2008
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| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Tyrosine--tRNA ligase, with EC number 6.1.1.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Tyrosyl t-RNA Synthetase from E.coli Complexed with Tyrosine
OverviewOverview
Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and KMSKS motifs that catalyze the amino acid activation with ATP. In the present study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly recognized by hydrogen bonds. This manner of hydrogen-bond recognition is conserved among the class I synthetases. Moreover, a comparison between the two structures revealed that the KMSKS loop is rearranged in response to adenine moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more compact ("semi-open") form, rather than the flexible, open form. The HIGH motif initially recognizes the gamma-phosphate, and then the alpha and gamma-phosphates of ATP, with a slight rearrangement of the residues. The other residues around the substrate also accommodate the Tyr-AMS. This induced-fit form presents a novel "snapshot" of the amino acid activation step in the aminoacylation reaction by TyrRS. The present structures and the T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive induced-fit conformational changes of the KMSKS loop and the local conformational changes within the substrate binding site form the basis for driving the amino acid activation step: the KMSKS loop adopts the open form, transiently shifts to the semi-open conformation according to the adenosyl moiety binding, and finally assumes the rigid ATP-bound, closed form. After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction.
About this StructureAbout this Structure
1X8X is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase., Kobayashi T, Takimura T, Sekine R, Kelly VP, Kamata K, Sakamoto K, Nishimura S, Yokoyama S, J Mol Biol. 2005 Feb 11;346(1):105-17. Epub 2004 Dec 15. PMID:15663931
Page seeded by OCA on Thu Mar 20 15:06:36 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Escherichia coli
- Single protein
- Tyrosine--tRNA ligase
- Kamata, K.
- Kelly, V P.
- Kobayashi, T.
- Nishimura, S.
- RSGI, RIKEN Structural Genomics/Proteomics Initiative.
- Sakamoto, K.
- Sekine, R.
- Takimura, T.
- Yokoyama, S.
- SO4
- TYR
- Ligase
- Riken structural genomics/proteomics initiative
- Rsgi
- Structural genomic