3ku4: Difference between revisions

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==Trapping of an oxocarbenium ion intermediate in UP crystals==
==Trapping of an oxocarbenium ion intermediate in UP crystals==
<StructureSection load='3ku4' size='340' side='right' caption='[[3ku4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='3ku4' size='340' side='right'caption='[[3ku4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3ku4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KU4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ku4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KU4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.099&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kuk|3kuk]], [[3kvr|3kvr]], [[3kvv|3kvv]], [[3kvy|3kvy]]</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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</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=3ku4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ku4 OCA], [https://pdbe.org/3ku4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ku4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ku4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ku4 ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ku4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ku4 OCA], [http://pdbe.org/3ku4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ku4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ku4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ku4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A5PJH9_BOVIN A5PJH9_BOVIN]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=3ku4 ConSurf].
</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=3ku4 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.
Glycal formation in crystals of uridine phosphorylase.,Paul D, O'Leary SE, Rajashankar K, Bu W, Toms A, Settembre EC, Sanders JM, Begley TP, Ealick SE Biochemistry. 2010 Apr 27;49(16):3499-509. PMID:20364833<ref>PMID:20364833</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ku4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Uridine phosphorylase|Uridine phosphorylase]]
*[[Uridine phosphorylase 3D structures|Uridine phosphorylase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bovin]]
[[Category: Bos taurus]]
[[Category: Uridine phosphorylase]]
[[Category: Large Structures]]
[[Category: Begley, T P]]
[[Category: Begley TP]]
[[Category: Bu, W]]
[[Category: Bu W]]
[[Category: Ealick, S E]]
[[Category: Ealick SE]]
[[Category: Leary, S O]]
[[Category: O'Leary S]]
[[Category: Paul, D]]
[[Category: Paul D]]
[[Category: Rajashankar, K]]
[[Category: Rajashankar K]]
[[Category: Sanders, J]]
[[Category: Sanders J]]
[[Category: Settembre, E]]
[[Category: Settembre E]]
[[Category: Toms, A]]
[[Category: Toms A]]
[[Category: Glycal]]
[[Category: Oxocarbenium ion]]
[[Category: Pyrimidine salvage]]
[[Category: Transferase]]

Latest revision as of 13:18, 21 February 2024

Trapping of an oxocarbenium ion intermediate in UP crystalsTrapping of an oxocarbenium ion intermediate in UP crystals

Structural highlights

3ku4 is a 4 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.099Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A5PJH9_BOVIN

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

3ku4, resolution 2.10Å

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