1d2r
From Proteopedia
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| - | [[Image:1d2r.jpg|left|200px]] | + | [[Image:1d2r.jpg|left|200px]] |
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| - | '''2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.''' | + | {{Structure |
| + | |PDB= 1d2r |SIZE=350|CAPTION= <scene name='initialview01'>1d2r</scene>, resolution 2.90Å | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= | ||
| + | }} | ||
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| + | '''2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1D2R is a [ | + | 1D2R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D2R OCA]. |
==Reference== | ==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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10716174 10716174] |
[[Category: Geobacillus stearothermophilus]] | [[Category: Geobacillus stearothermophilus]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: Ilyin, V A.]] | [[Category: Ilyin, V A.]] | ||
[[Category: Jr., C W.Carter.]] | [[Category: Jr., C W.Carter.]] | ||
| - | [[Category: | + | [[Category: aar]] |
[[Category: class i trna synthetase]] | [[Category: class i trna synthetase]] | ||
[[Category: induced fit]] | [[Category: induced fit]] | ||
| - | [[Category: | + | [[Category: trpr]] |
| - | ''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 10:32:05 2008'' |
Revision as of 08:32, 20 March 2008
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| , resolution 2.90Å | |||||||
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| Activity: | Tryptophan--tRNA ligase, with EC number 6.1.1.2 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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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