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| - | [[Image:2zim.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate== |
| - | |PDB= 2zim |SIZE=350|CAPTION= <scene name='initialview01'>2zim</scene>, resolution 2.10Å
| + | <StructureSection load='2zim' size='340' side='right'caption='[[2zim]], [[Resolution|resolution]] 2.10Å' scene=''> |
| - | |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>
| + | == Structural highlights == |
| - | |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>
| + | <table><tr><td colspan='2'>[[2zim]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZIM FirstGlance]. <br> |
| - | |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>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | |GENE= pylS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2209 Methanosarcina mazei])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zim OCA], [https://pdbe.org/2zim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zim RCSB], [https://www.ebi.ac.uk/pdbsum/2zim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zim ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[2q7g|2Q7G]], [[2q7e|2Q7E]], [[2q7h|2Q7H]]
| + | </table> |
| - | |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>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/PYLS_METMA PYLS_METMA] Catalyzes the attachment of pyrrolysine to tRNA(Pyl). Pyrrolysine is a lysine derivative encoded by the termination codon UAG (By similarity). |
| | + | == 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/zi/2zim_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=2zim ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''Pyrrolysyl-tRNA synthetase bound to adenylated pyrrolysine and pyrophosphate'''
| + | ==See Also== |
| - | | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | 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.
| + | [[Category: Large Structures]] |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 2ZIM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZIM OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | 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: Methanosarcina mazei]] |
| - | [[Category: Pyrrolysine--tRNA(Pyl) ligase]]
| + | [[Category: Kavran JM]] |
| - | [[Category: Single protein]]
| + | [[Category: Steitz TA]] |
| - | [[Category: Kavran, J M.]] | + | |
| - | [[Category: Steitz, T A.]] | + | |
| - | [[Category: aminoacyl-trna synthetase]]
| + | |
| - | [[Category: atp-binding]]
| + | |
| - | [[Category: cytoplasm]]
| + | |
| - | [[Category: ligase]]
| + | |
| - | [[Category: nucleotide-binding]]
| + | |
| - | [[Category: protein biosynthesis]]
| + | |
| - | [[Category: trna synthetase bound to an adenylated intermediate]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:20:58 2008''
| + | |
