2iy5

From Proteopedia

(Difference between revisions)

Current revision

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

Structural highlights

2iy5 is a 3 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYFA_THET8

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Moor N, Kotik-Kogan O, Tworowski D, Sukhanova M, Safro M. 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. Biochemistry. 2006 Sep 5;45(35):10572-83. PMID:16939209 doi:10.1021/bi060491l

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2iy5"

@@ Line 3: / Line 3: @@
 <StructureSection load='2iy5' size='340' side='right'caption='[[2iy5]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2iy5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IY5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2iy5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IY5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FYA:ADENOSINE-5-[PHENYLALANINOL-PHOSPHATE]'>FYA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1b70|1b70]], [[1b7y|1b7y]], [[2akw|2akw]], [[2aly|2aly]], [[2amc|2amc]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FYA:ADENOSINE-5-[PHENYLALANINOL-PHOSPHATE]'>FYA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phenylalanine--tRNA_ligase Phenylalanine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.20 6.1.1.20] </span></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2iy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iy5 OCA], [https://pdbe.org/2iy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iy5 RCSB], [https://www.ebi.ac.uk/pdbsum/2iy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iy5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYFA_THET8 SYFA_THET8]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 38: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Phenylalanine--tRNA ligase]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Thermus thermophilus]]
+[[Category: Kotik-Kogan O]]
-[[Category: Kotik-Kogan, O]]
+[[Category: Moor N]]
-[[Category: Moor, N]]
+[[Category: Safro M]]
-[[Category: Safro, M]]
+[[Category: Sukhanova M]]
-[[Category: Sukhanova, M]]
+[[Category: Tworowski D]]
-[[Category: Tworowski, D]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Atp-binding]]
-[[Category: Class ii aminoacyl-trna synthetase]]
-[[Category: Helix-turn-helix motif]]
-[[Category: Ligase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Phenylalanyl-trna synthetase]]
-[[Category: Protein biosynthesis]]
-[[Category: Rbd domin]]
-[[Category: Rna-binding]]
-[[Category: Sh3 domain]]
-[[Category: Trna-binding]]

2iy5

From Proteopedia

Current revision

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox