|
|
| (15 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| [[Image:1tn1.jpg|left|200px]]<br /><applet load="1tn1" size="450" color="white" frame="true" align="right" spinBox="true"
| |
| caption="1tn1, resolution 3.0Å" />
| |
| '''CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA'''<br />
| |
|
| |
|
| ==Overview== | | ==CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA== |
| X-ray diffraction data from monoclinic crystals of yeast tRNAPhe soaked in, dilute lead(II) acetate solutions at pH 5.0 and at pH 7.4 have been, collected to a resolution of 3 A, and the Pb(II) binding sites have been, obtained by difference Fourier analyses. The same three Pb(II) binding, sites are observed at both of these pH values. At pH 7.4 an extra peak of, negative electron density appears on the difference map close to one of, the Pb(II) binding sites and at the position of phosphate-18, indicating, cleavage of the sugar-phosphate-chain between residues D-17 and G-18 of, the tRNAPhe molecule in this derivative. Chain scission does not occur to, any observable extent in the structure at pH 5.0, and we have, therefore, a picture of the reactants (at pH 5.0) and products (at pH 7.4) of this, cleavage reaction. Polyacrylamide gel electrophoresis as well as, sequencing experiments confirms the cleavage of the tRNAPhe molecule into, one-fourth and three-fourth fragments, with the shorter fragment, consisting essentially of residues G-1 through D-17 while the larger, fragment contains residues G-18 through A-76. End-group analyses suggest a, ribose cyclic 2',3'-phosphate at D-17 of the one-fourth fragment with a, 5'-OH at G-18 of the three-fourth fragment. Cleavage of the tRNAPhe, molecule does not occur in the absence of Pb(II), and the proximity of one, of these metal ions to the cleavage site strongly implicates this metal, ion in the cleavage reaction. Consideration of several possible mechanisms, for the reaction, taking into account the biochemical and crystallographic, facts presented above, suggests that the cleavage involves removal of the, proton from the 2'-OH of ribose-17 by a Pb(II)-bound hydroxyl group., Subsequent nucleophilic attack of the resulting 2'-O- on the phosphorus, atom of phosphate-18, presumably through a pentacoordinate phosphorus, cyclic intermediate (as in the action of pancreatic ribonuclease A), results in chain scission. It cannot be decided whether the displacement, within the pentacoordinate intermediate, proceeds via an in-line or, adjacent pathway, but an exploration of the likelihood of either pathway, is presented. Strand cleavage at the particular site occurs fortuitously, because the aquo Pb(II) ion binds at the correct distance and presumably, in such a manner as to present a hydroxyl group in the correct orientation, to effect the proton abstraction.(ABSTRACT TRUNCATED AT 400 WORDS)
| | <StructureSection load='1tn1' size='340' side='right'caption='[[1tn1]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[1tn1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TN1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TN1 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]] 3Å</td></tr> |
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PB:LEAD+(II)+ION'>PB</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=YG:WYBUTOSINE'>YG</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=1tn1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tn1 OCA], [https://pdbe.org/1tn1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tn1 RCSB], [https://www.ebi.ac.uk/pdbsum/1tn1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tn1 ProSAT]</span></td></tr> |
| | </table> |
|
| |
|
| ==About this Structure== | | ==See Also== |
| 1TN1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with PB as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TN1 OCA].
| | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| | | __TOC__ |
| ==Reference==
| | </StructureSection> |
| Crystallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of yeast phenylalanine tRNA., Brown RS, Dewan JC, Klug A, Biochemistry. 1985 Aug 27;24(18):4785-801. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3907691 3907691]
| | [[Category: Large Structures]] |
| [[Category: Protein complex]] | | [[Category: Saccharomyces cerevisiae]] |
| [[Category: Brown, R.S.]] | | [[Category: Brown RS]] |
| [[Category: Dewan, J.C.]] | | [[Category: Dewan JC]] |
| [[Category: Hingerty, B.E.]] | | [[Category: Hingerty BE]] |
| [[Category: Klug, A.]] | | [[Category: Klug A]] |
| [[Category: PB]]
| |
| [[Category: t-rna]]
| |
| | |
| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:26:03 2007''
| |
