1gax: Difference between revisions

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Revision as of 20:40, 30 March 2008

File:1gax.gif

, resolution 2.9Å

Ligands:

, , , , ,

Activity:

Valine--tRNA ligase, with EC number 6.1.1.9

Related:

1ILE, 1QU2

Resources:

FirstGlance, OCA, PDBsum, RCSB

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 Sun Mar 30 20:40:21 2008

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

OCA

@@ Line 4: / Line 4: @@
 |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&#39;-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>
+|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=VAA:N-[VALINYL]-N&#39;-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]
+|ACTIVITY= <span class='plainlinks'>[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] </span>
 |GENE=
+|DOMAIN=
+|RELATEDENTRY=[[1ile|1ILE]], [[1qu2|1QU2]]
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gax OCA], [http://www.ebi.ac.uk/pdbsum/1gax PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1gax RCSB]</span>
 }}
@@ Line 32: / Line 35: @@
 [[Category: Vassylyev, D G.]]
 [[Category: Yokoyama, S.]]
-[[Category: VAA]]
-[[Category: ZN]]
 [[Category: coiled coil]]
 [[Category: protein-rna complex]]
@@ Line 42: / Line 43: @@
 [[Category: trna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 11:54:35 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:40:21 2008''