1fsi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (23:59, 20 November 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1fsi.png|left|200px]]
 
-
<!--
+
==CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA==
-
The line below this paragraph, containing "STRUCTURE_1fsi", creates the "Structure Box" on the page.
+
<StructureSection load='1fsi' size='340' side='right'caption='[[1fsi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1fsi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FSI FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_1fsi| PDB=1fsi | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1fsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fsi OCA], [https://pdbe.org/1fsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fsi RCSB], [https://www.ebi.ac.uk/pdbsum/1fsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fsi ProSAT]</span></td></tr>
 +
</table>
 +
== 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/fs/1fsi_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1fsi ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structure of the cyclic phosphodiesterase (CPDase) from Arabidopsis thaliana, an enzyme involved in the tRNA splicing pathway, was determined at 2.5 A resolution. CPDase hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr&gt;p), a product of the tRNA splicing reaction, to the monoester ADP-ribose 1"-phosphate (Appr-1"p). The 181 amino acid protein shows a novel, bilobal arrangement of two alphabeta modules. Each lobe consists of two alpha-helices on the outer side of the molecule, framing a three- or four-stranded antiparallel beta-sheet in the core of the protein. The active site is formed at the interface of the two beta-sheets in a water-filled cavity involving residues from two H-X-T/S-X motifs. This previously noticed motif participates in coordination of a sulfate ion. A solvent-exposed surface loop (residues 100-115) is very likely to play a flap-like role, opening and closing the active site. Based on the crystal structure and on recent mutagenesis studies of a homologous CPDase from Saccharomyces cerevisiae, we propose an enzymatic mechanism that employs the nucleophilic attack of a water molecule activated by one of the active site histidines.
-
===CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA===
+
Structure and mechanism of activity of the cyclic phosphodiesterase of Appr&gt;p, a product of the tRNA splicing reaction.,Hofmann A, Zdanov A, Genschik P, Ruvinov S, Filipowicz W, Wlodawer A EMBO J. 2000 Nov 15;19(22):6207-17. PMID:11080166<ref>PMID:11080166</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1fsi" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_11080166}}, adds the Publication Abstract to the page
+
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 11080166 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_11080166}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
1FSI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FSI OCA].
+
-
 
+
-
==Reference==
+
-
Structure and mechanism of activity of the cyclic phosphodiesterase of Appr&gt;p, a product of the tRNA splicing reaction., Hofmann A, Zdanov A, Genschik P, Ruvinov S, Filipowicz W, Wlodawer A, EMBO J. 2000 Nov 15;19(22):6207-17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11080166 11080166]
+
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Filipowicz, W.]]
+
[[Category: Filipowicz W]]
-
[[Category: Genschik, P.]]
+
[[Category: Genschik P]]
-
[[Category: Hofmann, A.]]
+
[[Category: Hofmann A]]
-
[[Category: Ruvinov, S.]]
+
[[Category: Ruvinov S]]
-
[[Category: Wlodawer, A.]]
+
[[Category: Wlodawer A]]
-
[[Category: Zdanov, A.]]
+
[[Category: Zdanov A]]
-
[[Category: 2',3'-cyclic nucleotide phosphodiesterase]]
+
-
[[Category: Adp-ribose 1'',2''-cyclic phosphate]]
+
-
[[Category: Appr>p]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 03:52:49 2008''
+

Current revision

CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA

PDB ID 1fsi

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1fsi"
Personal tools