2cyb: Difference between revisions

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Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus

OverviewOverview

Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play essential roles in the formation of the tyrosyl-adenylate from tyrosine and ATP. Here, we determined the crystal structures of Archaeoglobus fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which appears to correspond to the "semi-closed" form. This conformation enlarges the entrance to the tyrosine-binding pocket, which facilitates the pyrophosphate ion release after the tyrosyl-adenylate formation, and probably is involved in the initial tRNA binding. The KMSSS loop of the A.fulgidus TyrRS is somewhat farther from the active site and is stabilized by hydrogen bonds. Based on the three structures, possible structural changes of the KMSKS motif during the tyrosine activation reaction are discussed. We suggest that the insertion sequence just before the KMSKS motif, which exists in some archaeal species, enhances the binding affinity of the TyrRS for its cognate tRNA. In addition, a non-proline cis peptide bond, which is involved in the tRNA binding, is conserved among the archaeal TyrRSs.

About this StructureAbout this Structure

2CYB is a Single protein structure of sequence from Archaeoglobus fulgidus with as ligand. Active as Tyrosine--tRNA ligase, with EC number 6.1.1.1 Full crystallographic information is available from OCA.

ReferenceReference

Crystal structures of tyrosyl-tRNA synthetases from Archaea., Kuratani M, Sakai H, Takahashi M, Yanagisawa T, Kobayashi T, Murayama K, Chen L, Liu ZJ, Wang BC, Kuroishi C, Kuramitsu S, Terada T, Bessho Y, Shirouzu M, Sekine S, Yokoyama S, J Mol Biol. 2006 Jan 20;355(3):395-408. Epub 2005 Nov 14. PMID:16325203

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-[[Image:2cyb.gif|left|200px]]<br /><applet load="2cyb" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="2cyb, resolution 1.80&Aring;" />
 '''Crystal structure of Tyrosyl-tRNA Synthetase complexed with L-tyrosine from Archaeoglobus fulgidus'''<br />
 ==Overview==
-Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in, a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play, essential roles in the formation of the tyrosyl-adenylate from tyrosine, and ATP. Here, we determined the crystal structures of Archaeoglobus, fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at, 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix, TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS, motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS, loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which, appears to correspond to the "semi-closed" form. This conformation, enlarges the entrance to the tyrosine-binding pocket, which facilitates, the pyrophosphate ion release after the tyrosyl-adenylate formation, and, probably is involved in the initial tRNA binding. The KMSSS loop of the, A.fulgidus TyrRS is somewhat farther from the active site and is, stabilized by hydrogen bonds. Based on the three structures, possible, structural changes of the KMSKS motif during the tyrosine activation, reaction are discussed. We suggest that the insertion sequence just before, the KMSKS motif, which exists in some archaeal species, enhances the, binding affinity of the TyrRS for its cognate tRNA. In addition, a, non-proline cis peptide bond, which is involved in the tRNA binding, is, conserved among the archaeal TyrRSs.
+Tyrosyl-tRNA synthetase (TyrRS) catalyzes the tyrosylation of tRNA(Tyr) in a two-step reaction. TyrRS has the "HIGH" and "KMSKS" motifs, which play essential roles in the formation of the tyrosyl-adenylate from tyrosine and ATP. Here, we determined the crystal structures of Archaeoglobus fulgidus and Pyrococcus horikoshii TyrRSs in the l-tyrosine-bound form at 1.8A and 2.2A resolutions, respectively, and that of Aeropyrum pernix TyrRS in the substrate-free form at 2.2 A. The conformation of the KMSKS motif differs among the three TyrRSs. In the A.pernix TyrRS, the KMSKS loop conformation corresponds to the ATP-bound "closed" form. In contrast, the KMSKS loop of the P.horikoshii TyrRS forms a novel 3(10) helix, which appears to correspond to the "semi-closed" form. This conformation enlarges the entrance to the tyrosine-binding pocket, which facilitates the pyrophosphate ion release after the tyrosyl-adenylate formation, and probably is involved in the initial tRNA binding. The KMSSS loop of the A.fulgidus TyrRS is somewhat farther from the active site and is stabilized by hydrogen bonds. Based on the three structures, possible structural changes of the KMSKS motif during the tyrosine activation reaction are discussed. We suggest that the insertion sequence just before the KMSKS motif, which exists in some archaeal species, enhances the binding affinity of the TyrRS for its cognate tRNA. In addition, a non-proline cis peptide bond, which is involved in the tRNA binding, is conserved among the archaeal TyrRSs.
 ==About this Structure==
-CYB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] with TYR as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CYB OCA].
+CYB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] with <scene name='pdbligand=TYR:'>TYR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CYB OCA].
 ==Reference==
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 [[Category: Kobayashi, T.]]
 [[Category: Kuratani, M.]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
 [[Category: Sakai, H.]]
 [[Category: Shirouzu, M.]]
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 [[Category: structural genomics]]
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