2iy5: Difference between revisions
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
|PDB= 2iy5 |SIZE=350|CAPTION= <scene name='initialview01'>2iy5</scene>, resolution 3.10Å | |PDB= 2iy5 |SIZE=350|CAPTION= <scene name='initialview01'>2iy5</scene>, resolution 3.10Å | ||
|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Chain+B'>AC1</scene> | |SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Chain+B'>AC1</scene> | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=FYA:ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE]'>FYA</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> | ||
|ACTIVITY= [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] | |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> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|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> | |||
}} | }} | ||
| Line 28: | Line 31: | ||
[[Category: Sukhanova, M.]] | [[Category: Sukhanova, M.]] | ||
[[Category: Tworowski, D.]] | [[Category: Tworowski, D.]] | ||
[[Category: aminoacyl-trna synthetase]] | [[Category: aminoacyl-trna synthetase]] | ||
[[Category: atp-binding]] | [[Category: atp-binding]] | ||
| Line 46: | Line 47: | ||
[[Category: trna-binding]] | [[Category: trna-binding]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:50:22 2008'' | ||
Revision as of 03:50, 31 March 2008
| |||||||
| , resolution 3.10Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | , , , , , | ||||||
| Activity: | Phenylalanine--tRNA ligase, with EC number 6.1.1.20 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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 Mon Mar 31 03:50:22 2008
Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Phenylalanine--tRNA ligase
- Protein complex
- Thermus thermophilus
- Kotik-Kogan, O.
- Moor, N.
- Safro, M.
- Sukhanova, M.
- Tworowski, D.
- Aminoacyl-trna synthetase
- Atp-binding
- Class ii aminoacyl-trna synthetase
- Helix-turn-helix motif
- Ligase
- Magnesium
- Metal-binding
- Nucleotide-binding
- Phenylalanyl-trna synthetase
- Protein biosynthesis
- Rbd domin
- Rna-binding
- Sh3 domain
- Trna-binding