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'''Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase''' | '''Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase''' | ||
==Overview== | |||
Pyrrolysine, a lysine derivative with a bulky pyrroline ring, is the "22nd" genetically encoded amino acid. In the present study, the carboxy-terminal catalytic fragment of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) was analyzed by X-ray crystallography and site-directed mutagenesis. The catalytic fragment ligated tRNA(Pyl) with pyrrolysine nearly as efficiently as the full-length PylRS. We determined the crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, and compared them with the previously-reported PylRS structures. The ordering loop and the motif-2 loop undergo conformational changes from the "open" states to the "closed" states upon AMPPNP binding. On the other hand, the beta7-beta8 hairpin exhibits multiple conformational states, the open, intermediate (beta7-open/beta8-open and beta7-closed/beta8-open), and closed states, which are not induced upon substrate binding. The PylRS structures with a docked tRNA suggest that the active-site pocket can accommodate the CCA terminus of tRNA when the motif-2 loop is in the closed state and the beta7-beta8 hairpin is in the open or intermediate state. The entrance of the active-site pocket is nearly closed in the closed state of the beta7-beta8 hairpin, which may protect the pyrrolysyladenylate intermediate in the absence of tRNA(Pyl). Moreover, a structure-based mutational analysis revealed that hydrophobic residues in the amino acid-binding tunnel are important for accommodating the pyrrolysine side chain and that Asn346 is essential for anchoring the side-chain carbonyl and alpha-amino groups of pyrrolysine. In addition, a docking model of PylRS with tRNA was constructed based on the aspartyl-tRNA synthetase/tRNA structure, and was confirmed by a mutational analysis. | |||
==About this Structure== | ==About this Structure== | ||
2E3C is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. | 2E3C is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E3C OCA]. | ||
==Reference== | |||
Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase., Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S, J Mol Biol. 2008 Feb 29;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18387634 18387634] | |||
[[Category: Methanosarcina mazei]] | [[Category: Methanosarcina mazei]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Ishii, R.]] | [[Category: Ishii, R.]] | ||
| Line 24: | Line 26: | ||
[[Category: Yanagisawa, T.]] | [[Category: Yanagisawa, T.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
[[Category: | [[Category: Aminoacyl-trna synthetase]] | ||
[[Category: | [[Category: Ligase]] | ||
[[Category: | [[Category: National project on protein structural and functional analyse]] | ||
[[Category: | [[Category: Nppsfa]] | ||
[[Category: | [[Category: Pyrrolysine]] | ||
[[Category: | [[Category: Riken structural genomics/proteomics initiative]] | ||
[[Category: | [[Category: Rsgi]] | ||
[[Category: | [[Category: Structural genomic]] | ||
[[Category: | [[Category: Translation]] | ||
[[Category: | [[Category: Trna]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:24:24 2008'' | |||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | |||
Revision as of 06:24, 24 April 2008
Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase
Overview
Pyrrolysine, a lysine derivative with a bulky pyrroline ring, is the "22nd" genetically encoded amino acid. In the present study, the carboxy-terminal catalytic fragment of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS) was analyzed by X-ray crystallography and site-directed mutagenesis. The catalytic fragment ligated tRNA(Pyl) with pyrrolysine nearly as efficiently as the full-length PylRS. We determined the crystal structures of the PylRS catalytic fragment in the substrate-free, ATP analogue (AMPPNP)-bound, and AMPPNP/pyrrolysine-bound forms, and compared them with the previously-reported PylRS structures. The ordering loop and the motif-2 loop undergo conformational changes from the "open" states to the "closed" states upon AMPPNP binding. On the other hand, the beta7-beta8 hairpin exhibits multiple conformational states, the open, intermediate (beta7-open/beta8-open and beta7-closed/beta8-open), and closed states, which are not induced upon substrate binding. The PylRS structures with a docked tRNA suggest that the active-site pocket can accommodate the CCA terminus of tRNA when the motif-2 loop is in the closed state and the beta7-beta8 hairpin is in the open or intermediate state. The entrance of the active-site pocket is nearly closed in the closed state of the beta7-beta8 hairpin, which may protect the pyrrolysyladenylate intermediate in the absence of tRNA(Pyl). Moreover, a structure-based mutational analysis revealed that hydrophobic residues in the amino acid-binding tunnel are important for accommodating the pyrrolysine side chain and that Asn346 is essential for anchoring the side-chain carbonyl and alpha-amino groups of pyrrolysine. In addition, a docking model of PylRS with tRNA was constructed based on the aspartyl-tRNA synthetase/tRNA structure, and was confirmed by a mutational analysis.
About this Structure
2E3C is a Single protein structure of sequence from Methanosarcina mazei. Full crystallographic information is available from OCA.
Reference
Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase., Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S, J Mol Biol. 2008 Feb 29;. PMID:18387634 Page seeded by OCA on Thu Apr 24 09:24:24 2008
Proteopedia Page Contributors and Editors (what is this?)
- Pages with broken file links
- Methanosarcina mazei
- Single protein
- Ishii, R.
- RSGI, RIKEN Structural Genomics/Proteomics Initiative.
- Yanagisawa, T.
- Yokoyama, S.
- Aminoacyl-trna synthetase
- Ligase
- National project on protein structural and functional analyse
- Nppsfa
- Pyrrolysine
- Riken structural genomics/proteomics initiative
- Rsgi
- Structural genomic
- Translation
- Trna
