1m07: Difference between revisions

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<StructureSection load='1m07' size='340' side='right'caption='[[1m07]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1m07' size='340' side='right'caption='[[1m07]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1m07]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rana_catesbeiana Rana catesbeiana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M07 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M07 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1m07]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lithobates_catesbeianus Lithobates catesbeianus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M07 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M07 FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1km8|1km8]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </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=1m07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m07 OCA], [https://pdbe.org/1m07 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m07 RCSB], [https://www.ebi.ac.uk/pdbsum/1m07 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m07 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=1m07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m07 OCA], [https://pdbe.org/1m07 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m07 RCSB], [https://www.ebi.ac.uk/pdbsum/1m07 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m07 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RNASO_LITCT RNASO_LITCT]] Preferentially cleaves single-stranded RNA at pyrimidine residues with a 3'flanking guanine. Hydrolyzes poly(U) and poly(C) as substrates, and prefers the former. The S-lectins in frog eggs may be involved in the fertilization and development of the frog embryo. This lectin agglutinates various animal cells, including normal lymphocytes, erythrocytes, and fibroblasts of animal and human origin. It is cytotoxic against several tumor cells.  
[https://www.uniprot.org/uniprot/RNASO_LITCT RNASO_LITCT] Preferentially cleaves single-stranded RNA at pyrimidine residues with a 3'flanking guanine. Hydrolyzes poly(U) and poly(C) as substrates, and prefers the former. The S-lectins in frog eggs may be involved in the fertilization and development of the frog embryo. This lectin agglutinates various animal cells, including normal lymphocytes, erythrocytes, and fibroblasts of animal and human origin. It is cytotoxic against several tumor cells.
== 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=1m07 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=1m07 ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Rana catesbeiana (bullfrog) ribonucleases, which belong to the RNase A superfamily, exert cytotoxicity toward tumor cells. RC-RNase, the most active among frog ribonucleases, has a unique base preference for pyrimidine-guanine rather than pyrimidine-adenine in RNase A. Residues of RC-RNase involved in base specificity and catalytic activity were determined by site-directed mutagenesis, k(cat)/K(m) analysis toward dinucleotides, and cleavage site analysis of RNA substrate. The results show that Pyr-1 (N-terminal pyroglutamate), Lys-9, and Asn-38 along with His-10, Lys-35, and His-103 are involved in catalytic activity, whereas Pyr-1, Thr-39, Thr-70, Lys-95, and Glu-97 are involved in base specificity. The cytotoxicity of RC-RNase is correlated, but not proportional to, its catalytic activity. The crystal structure of the RC-RNase.d(ACGA) complex was determined at 1.80 A resolution. Residues Lys-9, His-10, Lys-35, and His-103 interacted directly with catalytic phosphate at the P(1) site, and Lys-9 was stabilized by hydrogen bonds contributed by Pyr-1, Tyr-28, and Asn-38. Thr-70 acts as a hydrogen bond donor for cytosine through Thr-39 and determines B(1) base specificity. Interestingly, Pyr-1 along with Lys-95 and Glu-97 form four hydrogen bonds with guanine at B(2) site and determine B(2) base specificity.
Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography.,Leu YJ, Chern SS, Wang SC, Hsiao YY, Amiraslanov I, Liaw YC, Liao YD J Biol Chem. 2003 Feb 28;278(9):7300-9. Epub 2002 Dec 23. PMID:12499382<ref>PMID:12499382</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1m07" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pancreatic ribonuclease]]
[[Category: Lithobates catesbeianus]]
[[Category: Rana catesbeiana]]
[[Category: Amiraslanov I]]
[[Category: Amiraslanov, I]]
[[Category: Chern S-S]]
[[Category: Chern, S S]]
[[Category: Hsiao Y-Y]]
[[Category: Hsiao, Y Y]]
[[Category: Leu Y-J]]
[[Category: Leu, Y J]]
[[Category: Liao Y-D]]
[[Category: Liao, Y D]]
[[Category: Liaw Y-C]]
[[Category: Liaw, Y C]]
[[Category: Wang S-C]]
[[Category: Wang, S C]]
[[Category: Bullfrog]]
[[Category: Cytotoxicity]]
[[Category: Hydrolase-dna complex]]
[[Category: Ribonuclease]]
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