2zim: Difference between revisions

Revision as of 20:13, 4 May 2008

Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate

OverviewOverview

Pyrrolysine (Pyl), the 22nd natural amino acid and genetically encoded by UAG, becomes attached to its cognate tRNA by pyrrolysyl-tRNA synthetase (PylRS). We have determined three crystal structures of the Methanosarcina mazei PylRS complexed with either AMP-PNP, Pyl-AMP plus pyrophosphate, or the Pyl analogue N-epsilon-[(cylopentyloxy)carbonyl]-L-lysine plus ATP. The structures reveal that PylRS utilizes a deep hydrophobic pocket for recognition of the Pyl side chain. A comparison of these structures with previously determined class II tRNA synthetase complexes illustrates that different substrate specificities derive from changes in a small number of residues that form the substrate side-chain-binding pocket. The knowledge of these structures allowed the placement of PylRS in the aminoacyl-tRNA synthetase (aaRS) tree as the last known synthetase that evolved for genetic code expansion, as well as the finding that Pyl arose before the last universal common ancestral state. The PylRS structure provides an excellent framework for designing new aaRSs with altered amino acid specificity.

About this StructureAbout this Structure

2ZIM is a Single protein structure of sequence from Methanosarcina mazei. Full crystallographic information is available from OCA.

ReferenceReference

Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation., Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Soll D, Steitz TA, Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11268-73. Epub 2007 Jun 25. PMID:17592110 Page seeded by OCA on Sun May 4 20:13:35 2008

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

OCA

@@ Line 1: / Line 1: @@
 [[Image:2zim.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2zim |SIZE=350|CAPTION= <scene name='initialview01'>2zim</scene>, resolution 2.10&Aring;
+The line below this paragraph, containing "STRUCTURE_2zim", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:Edo+Binding+Site+For+Residue+A+902'>AC1</scene>, <scene name='pdbsite=AC2:Edo+Binding+Site+For+Residue+A+903'>AC2</scene>, <scene name='pdbsite=AC3:Edo+Binding+Site+For+Residue+A+904'>AC3</scene>, <scene name='pdbsite=AC4:Edo+Binding+Site+For+Residue+A+905'>AC4</scene>, <scene name='pdbsite=AC5:Edo+Binding+Site+For+Residue+A+906'>AC5</scene>, <scene name='pdbsite=AC6:Edo+Binding+Site+For+Residue+A+907'>AC6</scene>, <scene name='pdbsite=AC7:Edo+Binding+Site+For+Residue+A+908'>AC7</scene>, <scene name='pdbsite=AC8:Edo+Binding+Site+For+Residue+A+909'>AC8</scene>, <scene name='pdbsite=AC9:Edo+Binding+Site+For+Residue+A+910'>AC9</scene>, <scene name='pdbsite=BC1:Edo+Binding+Site+For+Residue+A+911'>BC1</scene>, <scene name='pdbsite=BC2:Yly+Binding+Site+For+Residue+A+1'>BC2</scene> and <scene name='pdbsite=BC3:Pop+Binding+Site+For+Residue+A+901'>BC3</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene>, <scene name='pdbligand=YLY:(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL+[(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+HYDROGEN+(R)-PHOSPHATE'>YLY</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyrrolysine--tRNA(Pyl)_ligase Pyrrolysine--tRNA(Pyl) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.26 6.1.1.26] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei])
+-->
-|DOMAIN=
+{{STRUCTURE_2zim|  PDB=2zim  |  SCENE=  }}
-|RELATEDENTRY=[[2q7g|2Q7G]], [[2q7e|2Q7E]], [[2q7h|2Q7H]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zim OCA], [http://www.ebi.ac.uk/pdbsum/2zim PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2zim RCSB]</span>
-}}
 '''Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate'''
@@ Line 24: / Line 21: @@
 Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation., Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Soll D, Steitz TA, Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11268-73. Epub 2007 Jun 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17592110 17592110]
 [[Category: Methanosarcina mazei]]
-[[Category: Pyrrolysine--tRNA(Pyl) ligase]]
 [[Category: Single protein]]
 [[Category: Kavran, J M.]]
 [[Category: Steitz, T A.]]
-[[Category: aminoacyl-trna synthetase]]
+[[Category: Aminoacyl-trna synthetase]]
-[[Category: atp-binding]]
+[[Category: Atp-binding]]
-[[Category: cytoplasm]]
+[[Category: Cytoplasm]]
-[[Category: ligase]]
+[[Category: Ligase]]
-[[Category: nucleotide-binding]]
+[[Category: Nucleotide-binding]]
-[[Category: protein biosynthesis]]
+[[Category: Protein biosynthesis]]
-[[Category: trna synthetase bound to an adenylated intermediate]]
+[[Category: Trna synthetase bound to an adenylated intermediate]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:13:35 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:20:58 2008''