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| - | [[Image:2zcd.jpg|left|200px]] | + | #REDIRECT [[3vqv]] This PDB entry is obsolete and replaced by 3vqv |
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| - | {{STRUCTURE_2zcd| PDB=2zcd | SCENE= }}
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| - | '''Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with AMPPNP'''
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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.
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| - | ==About this Structure==
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| - | 2ZCD 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=2ZCD OCA].
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| - | ==Reference==
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| - | 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]
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| - | [[Category: Methanosarcina mazei]]
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| - | [[Category: Single protein]]
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| - | [[Category: Ishii, R.]]
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| - | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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| - | [[Category: Yanagisawa, T.]]
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| - | [[Category: Yokoyama, S.]]
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| - | [[Category: Aminoacyl-trna synthetase]]
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| - | [[Category: Atp analogue]]
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| - | [[Category: Atp-binding]]
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| - | [[Category: Cytoplasm]]
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| - | [[Category: Ligase]]
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| - | [[Category: National project on protein structural and functional analyse]]
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| - | [[Category: Nppsfa]]
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| - | [[Category: Nucleotide-binding]]
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| - | [[Category: Protein biosynthesis]]
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| - | [[Category: Protein3000]]
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| - | [[Category: Pyrrolysyl-trna synthetase]]
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| - | [[Category: Riken structural genomics/proteomics initiative]]
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| - | [[Category: Rsgi]]
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| - | [[Category: Structural genomic]]
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| - | [[Category: Trna]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:45:12 2008''
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