1asz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /> <applet load="1asz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1asz, resolution 3.0&Aring;" /> '''THE ACTIVE SITE OF Y...)
Current revision (06:33, 7 February 2024) (edit) (undo)
 
(20 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1asz.gif|left|200px]]<br />
 
-
<applet load="1asz" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1asz, resolution 3.0&Aring;" />
 
-
'''THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION'''<br />
 
-
==Overview==
+
==THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION==
-
The crystal structures of the various complexes formed by yeast, aspartyl-tRNA synthetase (AspRS) and its substrates provide snapshots of, the active site corresponding to different steps of the aminoacylation, reaction. Native crystals of the binary complex tRNA-AspRS were soaked in, solutions containing the two other substrates, ATP (or its analog AMPPcP), and aspartic acid. When all substrates are present in the crystal, this, leads to the formation of the aspartyl-adenylate and/or the aspartyl-tRNA., A class II-specific pathway for the aminoacylation reaction is proposed, which explains the known functional differences between the two classes, while preserving a common framework. Extended signature sequences, characteristic of class II aaRS (motifs 2 and 3) constitute the basic, functional unit. The ATP molecule adopts a bent conformation, stabilized, by the invariant Arg531 of motif 3 and a magnesium ion coordinated to the, pyrophosphate group and to two class-invariant acidic residues. The, aspartic acid substrate is positioned by a class II invariant acidic, residue, Asp342, interacting with the amino group and by amino acids, conserved in the aspartyl synthetase family. The amino acids in contact, with the substrates have been probed by site-directed mutagenesis for, their functional implication.
+
<StructureSection load='1asz' size='340' side='right'caption='[[1asz]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1asz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. The April 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aminoacyl-tRNA Synthetases'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_4 10.2210/rcsb_pdb/mom_2001_4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ASZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ASZ FirstGlance]. <br>
 +
</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&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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=1asz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1asz OCA], [https://pdbe.org/1asz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1asz RCSB], [https://www.ebi.ac.uk/pdbsum/1asz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1asz ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SYDC_YEAST SYDC_YEAST]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/as/1asz_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1asz ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1ASZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with ATP as [http://en.wikipedia.org/wiki/ligand ligand]. The following page contains interesting information on the relation of 1ASZ with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb16_1.html Aminoacyl-tRNA Synthetases]]. Active as [http://en.wikipedia.org/wiki/Aspartate--tRNA_ligase Aspartate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.12 6.1.1.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ASZ OCA].
+
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-
 
+
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-
==Reference==
+
__TOC__
-
The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction., Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry JC, Moras D, EMBO J. 1994 Jan 15;13(2):327-37. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8313877 8313877]
+
</StructureSection>
[[Category: Aminoacyl-tRNA Synthetases]]
[[Category: Aminoacyl-tRNA Synthetases]]
-
[[Category: Aspartate--tRNA ligase]]
+
[[Category: Large Structures]]
 +
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Single protein]]
+
[[Category: Cavarelli J]]
-
[[Category: Cavarelli, J.]]
+
[[Category: Moras D]]
-
[[Category: Moras, D.]]
+
[[Category: Rees B]]
-
[[Category: Rees, B.]]
+
[[Category: Thierry JC]]
-
[[Category: Thierry, J.C.]]
+
-
[[Category: ATP]]
+
-
[[Category: complex (aminoacyl-trna synthase/trna)]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 08:57:08 2007''
+

Current revision

THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION

PDB ID 1asz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1asz"
Personal tools