2iy5: Difference between revisions

Revision as of 08:04, 4 May 2008

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH TRNA AND A PHENYLALANYL-ADENYLATE ANALOG

OverviewOverview

The crystal structure of the ternary complex of (alphabeta)(2) heterotetrameric phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus with cognate tRNA(Phe) and a nonhydrolyzable phenylalanyl-adenylate analogue (PheOH-AMP) has been determined at 3.1 A resolution. It reveals conformational changes in tRNA(Phe) induced by the PheOH-AMP binding. The single-stranded 3' end exhibits a hairpin conformation in contrast to the partial unwinding observed previously in the binary PheRS.tRNA(Phe) complex. The CCA end orientation is stabilized by extensive base-specific interactions of A76 and C75 with the protein and by intra-RNA interactions of A73 with adjacent nucleotides. The 4-amino group of the "bulged out" C75 is trapped by two negatively charged residues of the beta subunit (Glubeta31 and Aspbeta33), highly conserved in eubacterial PheRSs. The position of the A76 base is stabilized by interactions with Hisalpha212 of motif 2 (universally conserved in PheRSs) and class II-invariant Argalpha321 of motif 3. Important conformational changes induced by the binding of tRNA(Phe) and PheOH-AMP are observed in the catalytic domain: the motif 2 loop and a "helical" loop (residues 139-152 of the alpha subunit) undergo coordinated displacement; Metalpha148 of the helical loop adopts a conformation preventing the 2'-OH group of A76 from approaching the alpha-carbonyl carbon of PheOH-AMP. The unfavorable position of the terminal ribose stems from the absence of the alpha-carbonyl oxygen in the analogue. Our data suggest that the idiosyncratic feature of PheRS, which aminoacylates the 2'-OH group of the terminal ribose, is dictated by the system-specific topology of the CCA end-binding site.

About this StructureAbout this Structure

2IY5 is a Protein complex structure of sequences from Thermus thermophilus. Full crystallographic information is available from OCA.

ReferenceReference

The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end., Moor N, Kotik-Kogan O, Tworowski D, Sukhanova M, Safro M, Biochemistry. 2006 Sep 5;45(35):10572-83. PMID:16939209 Page seeded by OCA on Sun May 4 08:04:01 2008

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OCA

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 [[Image:2iy5.gif|left|200px]]
- {{Structure
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+The line below this paragraph, containing "STRUCTURE_2iy5", creates the "Structure Box" on the page.
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-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylalanine--tRNA_ligase Phenylalanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.20 6.1.1.20] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2iy5|  PDB=2iy5  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2iy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iy5 OCA], [http://www.ebi.ac.uk/pdbsum/2iy5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2iy5 RCSB]</span>
-}}
 '''PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH TRNA AND A PHENYLALANYL-ADENYLATE ANALOG'''
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 [[Category: Sukhanova, M.]]
 [[Category: Tworowski, D.]]
-[[Category: aminoacyl-trna synthetase]]
+[[Category: Aminoacyl-trna synthetase]]
-[[Category: atp-binding]]
+[[Category: Atp-binding]]
-[[Category: class ii aminoacyl-trna synthetase]]
+[[Category: Class ii aminoacyl-trna synthetase]]
-[[Category: helix-turn-helix motif]]
+[[Category: Helix-turn-helix motif]]
-[[Category: ligase]]
+[[Category: Ligase]]
-[[Category: magnesium]]
+[[Category: Magnesium]]
-[[Category: metal-binding]]
+[[Category: Metal-binding]]
-[[Category: nucleotide-binding]]
+[[Category: Nucleotide-binding]]
-[[Category: phenylalanyl-trna synthetase]]
+[[Category: Phenylalanyl-trna synthetase]]
-[[Category: protein biosynthesis]]
+[[Category: Protein biosynthesis]]
-[[Category: rbd domin]]
+[[Category: Rbd domin]]
-[[Category: rna-binding]]
+[[Category: Rna-binding]]
-[[Category: sh3 domain]]
+[[Category: Sh3 domain]]
-[[Category: thermus thermophilus]]
+[[Category: Thermus thermophilus]]
-[[Category: trna-binding]]
+[[Category: Trna-binding]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 08:04:01 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:50:22 2008''