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| {{STRUCTURE_2zce| PDB=2zce | SCENE= }} | | {{STRUCTURE_2zce| PDB=2zce | SCENE= }} |
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| '''Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with pyrrolysine and an ATP analogue'''
| | ===Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with pyrrolysine and an ATP analogue=== |
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| ==Overview==
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| 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.
| | The line below this paragraph, {{ABSTRACT_PUBMED_18387634}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 18387634 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_18387634}} |
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| ==About this Structure== | | ==About this Structure== |
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| [[Category: Structural genomic]] | | [[Category: Structural genomic]] |
| [[Category: Trna]] | | [[Category: Trna]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:45:13 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:24:36 2008'' |
