1d2r
From Proteopedia
(New page: 200px<br /><applet load="1d2r" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d2r, resolution 2.90Å" /> '''2.9 A CRYSTAL STRUCT...) |
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| - | [[Image:1d2r.jpg|left|200px]]<br /><applet load="1d2r" size=" | + | [[Image:1d2r.jpg|left|200px]]<br /><applet load="1d2r" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1d2r, resolution 2.90Å" /> | caption="1d2r, resolution 2.90Å" /> | ||
'''2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.'''<br /> | '''2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) | + | The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) was solved at 2.9 A using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5'AMP complex (TAM; Doublie S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17-31). In agreement with small-angle solution X-ray scattering experiments, unliganded TrpRS has a conformation in which both monomers open, leaving only the tryptophan-binding regions of their active sites intact. The amino terminal alphaA-helix, TIGN, and KMSKS signature sequences, and the distal helical domain rotate as a single rigid body away from the dinucleotide-binding fold domain, opening the AMP binding site, seen in the TAM complex, into two halves. Comparison of side-chain packing in ligand-free TrpRS and the TAM complex, using identification of nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189-1195), shows that significant repacking occurs between three relatively stable core regions, one of which acts as a bearing between the other two. These domain rearrangements provide a new structural paradigm that is consistent in detail with the "induced-fit" mechanism proposed for TyrRS by Fersht et al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G, 1988, Biochemistry 27:1581-1587). Coupling of ATP binding determinants associated with the two catalytic signature sequences to the helical domain containing the presumptive anticodon-binding site provides a mechanism to coordinate active-site chemistry with relocation of the major tRNA binding determinants. |
==About this Structure== | ==About this Structure== | ||
| - | 1D2R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Active as [http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] Full crystallographic information is available from [http:// | + | 1D2R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Active as [http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D2R OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Tryptophan--tRNA ligase]] | [[Category: Tryptophan--tRNA ligase]] | ||
| - | [[Category: Ilyin, V | + | [[Category: Ilyin, V A.]] |
| - | [[Category: Jr., C | + | [[Category: Jr., C W.Carter.]] |
[[Category: aars]] | [[Category: aars]] | ||
[[Category: class i trna synthetase]] | [[Category: class i trna synthetase]] | ||
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[[Category: trprs]] | [[Category: trprs]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:12:20 2008'' |
Revision as of 10:12, 21 February 2008
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2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.
Overview
The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) was solved at 2.9 A using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5'AMP complex (TAM; Doublie S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17-31). In agreement with small-angle solution X-ray scattering experiments, unliganded TrpRS has a conformation in which both monomers open, leaving only the tryptophan-binding regions of their active sites intact. The amino terminal alphaA-helix, TIGN, and KMSKS signature sequences, and the distal helical domain rotate as a single rigid body away from the dinucleotide-binding fold domain, opening the AMP binding site, seen in the TAM complex, into two halves. Comparison of side-chain packing in ligand-free TrpRS and the TAM complex, using identification of nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189-1195), shows that significant repacking occurs between three relatively stable core regions, one of which acts as a bearing between the other two. These domain rearrangements provide a new structural paradigm that is consistent in detail with the "induced-fit" mechanism proposed for TyrRS by Fersht et al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G, 1988, Biochemistry 27:1581-1587). Coupling of ATP binding determinants associated with the two catalytic signature sequences to the helical domain containing the presumptive anticodon-binding site provides a mechanism to coordinate active-site chemistry with relocation of the major tRNA binding determinants.
About this Structure
1D2R is a Single protein structure of sequence from Geobacillus stearothermophilus. Active as Tryptophan--tRNA ligase, with EC number 6.1.1.2 Full crystallographic information is available from OCA.
Reference
2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site., Ilyin VA, Temple B, Hu M, Li G, Yin Y, Vachette P, Carter CW Jr, Protein Sci. 2000 Feb;9(2):218-31. PMID:10716174
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