6pgl

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:54, 13 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6pgl' size='340' side='right'caption='[[6pgl]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
<StructureSection load='6pgl' size='340' side='right'caption='[[6pgl]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6pgl]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Candida_kefyr Candida kefyr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PGL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PGL FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6pgl]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_marxianus_DMKU3-1042 Kluyveromyces marxianus DMKU3-1042]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PGL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PGL FirstGlance]. <br>
-
</td></tr><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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.845&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KLMA_50491 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1003335 Candida kefyr])</td></tr>
+
<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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6pgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pgl OCA], [http://pdbe.org/6pgl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pgl RCSB], [http://www.ebi.ac.uk/pdbsum/6pgl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pgl ProSAT]</span></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=6pgl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pgl OCA], [https://pdbe.org/6pgl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pgl RCSB], [https://www.ebi.ac.uk/pdbsum/6pgl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pgl ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/W0TCJ5_KLUMD W0TCJ5_KLUMD]
-
U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n - 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.
+
-
 
+
-
Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.,Nomura Y, Montemayor EJ, Virta JM, Hayes SM, Butcher SE Nucleic Acids Res. 2020 Feb 20;48(3):1423-1434. doi: 10.1093/nar/gkz1177. PMID:31832688<ref>PMID:31832688</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 6pgl" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Candida kefyr]]
+
[[Category: Kluyveromyces marxianus DMKU3-1042]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Butcher, S E]]
+
[[Category: Butcher SE]]
-
[[Category: Montemayor, E J]]
+
[[Category: Montemayor EJ]]
-
[[Category: Nomura, Y]]
+
[[Category: Nomura Y]]
-
[[Category: 2h phosphodiesterase superfamily]]
+
-
[[Category: Exonuclease]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: U6 snrna]]
+

Current revision

Structure of Kluyveromyces marxianus Usb1 with uridine monophosphate

PDB ID 6pgl

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/6pgl"
Personal tools