1gax: Difference between revisions

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Revision as of 12:20, 20 March 2008

File:1gax.gif

, resolution 2.9Å

Ligands:

and

Activity:

Valine--tRNA ligase, with EC number 6.1.1.9

Coordinates:

save as pdb, mmCIF, xml

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

OverviewOverview

Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.

About this StructureAbout this Structure

1GAX is a Single protein structure of sequence from Thermus thermophilus. The following page contains interesting information on the relation of 1GAX with [Aminoacyl-tRNA Synthetases]. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S, Cell. 2000 Nov 22;103(5):793-803. PMID:11114335

Page seeded by OCA on Thu Mar 20 11:20:40 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1gax.gif|left|200px]]<br /><applet load="1gax" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1gax.gif|left|200px]]
-caption="1gax, resolution 2.9&Aring;" />
-'''CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE'''<br />
+ {{Structure
+|PDB= 1gax |SIZE=350|CAPTION= <scene name='initialview01'>1gax</scene>, resolution 2.9&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=VAA:N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9]
+|GENE=
+}}
+'''CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-GAX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=VAA:'>VAA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. The following page contains interesting information on the relation of 1GAX 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/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA].
+GAX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The following page contains interesting information on the relation of 1GAX with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb16_1.html Aminoacyl-tRNA Synthetases]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAX OCA].
 ==Reference==
-Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S, Cell. 2000 Nov 22;103(5):793-803. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11114335 11114335]
+Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Tao J, Vassylyev DG, Yokoyama S, Cell. 2000 Nov 22;103(5):793-803. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11114335 11114335]
 [[Category: Aminoacyl-tRNA Synthetases]]
 [[Category: Single protein]]
@@ Line 30: / Line 39: @@
 [[Category: rossmann fold]]
 [[Category: rsgi]]
-[[Category: structural genomics]]
+[[Category: structural genomic]]
 [[Category: trna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:48:13 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:20:40 2008''