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1w4q

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[[Image:1w4q.gif|left|200px]]
 
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{{Structure
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==Binding of Nonnatural 3'-Nucleotides to Ribonuclease A==
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|PDB= 1w4q |SIZE=350|CAPTION= <scene name='initialview01'>1w4q</scene>, resolution 1.68&Aring;
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<StructureSection load='1w4q' size='340' side='right'caption='[[1w4q]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Umf+Binding+Site+For+Chain+B'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=UMF:2'-FLUORO-2'-DEOXYURIDINE 3'-MONOPHOSPHATE'>UMF</scene>
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<table><tr><td colspan='2'>[[1w4q]] is a 2 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=1W4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W4Q FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.68&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UMF:2-FLUORO-2-DEOXYURIDINE+3-MONOPHOSPHATE'>UMF</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1w4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w4q OCA], [https://pdbe.org/1w4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w4q RCSB], [https://www.ebi.ac.uk/pdbsum/1w4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w4q ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w4/1w4q_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1w4q ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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2'-Fluoro-2'-deoxyuridine 3'-phosphate (dU(F)MP) and arabinouridine 3'-phosphate (araUMP) have non-natural furanose rings. dU(F)MP and araUMP were prepared by chemical synthesis and found to have three- to sevenfold higher affinity than uridine 3'-phosphate (3'-UMP) or 2'-deoxyuridine 3'-phosphate (dUMP) for ribonuclease A (RNase A). These differences probably arise (in part) from the phosphoryl groups of 3'-UMP, dU(F)MP, and araUMP (pK(a) = 5.9) being more anionic than that of dUMP (pK(a) = 6.3). The three-dimensional structures of the crystalline complexes of RNase A with dUMP, dU(F)MP and araUMP were determined at &lt; 1.7 A resolution by X-ray diffraction analysis. In these three structures, the uracil nucleobases and phosphoryl groups bind to the enzyme in a nearly identical position. Unlike 3'-UMP and dU(F)MP, dUMP and araUMP bind with their furanose rings in the preferred pucker. In the RNase A.araUMP complex, the 2'-hydroxyl group is exposed to the solvent. All four 3'-nucleotides bind more tightly to wild-type RNase A than to its T45G variant, which lacks the residue that interacts most closely with the uracil nucleobase. These findings illuminate in atomic detail the interaction of RNase A and 3'-nucleotides, and indicate that non-natural furanose rings can serve as the basis for more potent inhibitors of catalysis by RNase A.
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'''BINDING OF NONNATURAL 3'-NUCLEOTIDES TO RIBONUCLEASE A'''
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Binding of non-natural 3'-nucleotides to ribonuclease A.,Jenkins CL, Thiyagarajan N, Sweeney RY, Guy MP, Kelemen BR, Acharya KR, Raines RT FEBS J. 2005 Feb;272(3):744-55. PMID:15670155<ref>PMID:15670155</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1w4q" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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2'-Fluoro-2'-deoxyuridine 3'-phosphate (dU(F)MP) and arabinouridine 3'-phosphate (araUMP) have non-natural furanose rings. dU(F)MP and araUMP were prepared by chemical synthesis and found to have three- to sevenfold higher affinity than uridine 3'-phosphate (3'-UMP) or 2'-deoxyuridine 3'-phosphate (dUMP) for ribonuclease A (RNase A). These differences probably arise (in part) from the phosphoryl groups of 3'-UMP, dU(F)MP, and araUMP (pK(a) = 5.9) being more anionic than that of dUMP (pK(a) = 6.3). The three-dimensional structures of the crystalline complexes of RNase A with dUMP, dU(F)MP and araUMP were determined at &lt; 1.7 A resolution by X-ray diffraction analysis. In these three structures, the uracil nucleobases and phosphoryl groups bind to the enzyme in a nearly identical position. Unlike 3'-UMP and dU(F)MP, dUMP and araUMP bind with their furanose rings in the preferred pucker. In the RNase A.araUMP complex, the 2'-hydroxyl group is exposed to the solvent. All four 3'-nucleotides bind more tightly to wild-type RNase A than to its T45G variant, which lacks the residue that interacts most closely with the uracil nucleobase. These findings illuminate in atomic detail the interaction of RNase A and 3'-nucleotides, and indicate that non-natural furanose rings can serve as the basis for more potent inhibitors of catalysis by RNase A.
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1W4Q is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W4Q OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Binding of non-natural 3'-nucleotides to ribonuclease A., Jenkins CL, Thiyagarajan N, Sweeney RY, Guy MP, Kelemen BR, Acharya KR, Raines RT, FEBS J. 2005 Feb;272(3):744-55. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15670155 15670155]
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[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Pancreatic ribonuclease]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Acharya KR]]
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[[Category: Acharya, K R.]]
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[[Category: Guy MP]]
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[[Category: Guy, M P.]]
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[[Category: Jenkins CL]]
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[[Category: Jenkins, C L.]]
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[[Category: Kelemen BR]]
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[[Category: Kelemen, B R.]]
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[[Category: Raines RT]]
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[[Category: Raines, R T.]]
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[[Category: Sweeney RY]]
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[[Category: Sweeney, R Y.]]
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[[Category: Thiyagarajan N]]
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[[Category: Thiyagarajan, N.]]
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[[Category: UMF]]
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[[Category: endonuclease]]
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[[Category: hydrolase]]
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[[Category: nonnatural 3'-nucleotide]]
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[[Category: ribonuclease]]
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[[Category: rnase some]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:52:09 2008''
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Current revision

Binding of Nonnatural 3'-Nucleotides to Ribonuclease A

PDB ID 1w4q

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