1d2r

[[Image:1d2r.jpg|left|200px]]

|PDB= 1d2r |SIZE=350|CAPTION= <scene name='initialview01'>1d2r</scene>, resolution 2.90&Aring;

|SITE=

|LIGAND=

|ACTIVITY= <span class='plainlinks'>[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] </span>

|GENE=

|DOMAIN=

|RELATEDENTRY=

|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d2r OCA], [http://www.ebi.ac.uk/pdbsum/1d2r PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d2r RCSB]</span>

 

 

==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.

 

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].

 

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: Single protein]]

[[Category: Tryptophan--tRNA ligase]]

[[Category: Ilyin, V A.]]