1uca: Difference between revisions
No edit summary |
No edit summary |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 2'-UMP== | |||
<StructureSection load='1uca' size='340' side='right'caption='[[1uca]], [[Resolution|resolution]] 1.48Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1uca]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Momordica_charantia Momordica charantia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UCA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UCA FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.48Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U2P:PHOSPHORIC+ACID+MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL]+ESTER'>U2P</scene></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=1uca FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uca OCA], [https://pdbe.org/1uca PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uca RCSB], [https://www.ebi.ac.uk/pdbsum/1uca PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uca ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RNMC1_MOMCH RNMC1_MOMCH] Ribonuclease cleaving preferentially the 5'-side of uridine.<ref>PMID:10964705</ref> | |||
== 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/uc/1uca_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=1uca ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ribonuclease MC1 (RNase MC1) isolated from seeds of bitter gourd (Momordica charantia) consists of 190 amino acids and is characterized by a preferential cleavage at the 5'-side of uridine. This uridine specificity distinguishes RNase MC1 from other enzymes belonging to the RNase T2 family. The three-dimensional structures of RNase MC1, in a complex with either 2'-UMP or 3'-UMP, were determined at 1.48 and 1.77 A resolutions, respectively. The side chains of Gln9 and Asn71 interact with O4 and N3, respectively, of the uracil base by hydrogen bondings. In addition, the uracil base is sandwiched by the hydrophobic side chains of Leu73 and Phe80. Compared with these amino acid residues and corresponding residues in RNases in the RNase T2 family, Gln9 and Phe80 are highly conserved in the RNases in T2 family, while Asn71 and Leu73 in RNase MC1 are variant in sequences. It is thus likely that interactions of the side chains of Asn71 and Leu73 with the uracil base are responsible for the absolute uridine specificity of RNase MC1. Site-directed mutagenesis experiments showed that replacement of Asn by Thr decreased both the catalytic efficiency and the binding affinity by 2.3- and 7.0-fold, respectively, and substitution of Leu73 for Ala predominantly decreased the binding affinity by 14. 5-fold, compared with findings in case of wild-type RNase MC1. It is thus demonstrated that Asn71 and Leu73 play an essential role in uridine preference for RNase MC1. | |||
Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity.,Suzuki A, Yao M, Tanaka I, Numata T, Kikukawa S, Yamasaki N, Kimura M Biochem Biophys Res Commun. 2000 Aug 28;275(2):572-6. PMID:10964705<ref>PMID:10964705</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1uca" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Ribonuclease|Ribonuclease]] | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Momordica charantia]] | [[Category: Momordica charantia]] | ||
[[Category: Kikukawa | [[Category: Kikukawa S]] | ||
[[Category: Kimura | [[Category: Kimura M]] | ||
[[Category: Numata | [[Category: Numata T]] | ||
[[Category: Suzuki | [[Category: Suzuki A]] | ||
[[Category: Tanaka | [[Category: Tanaka I]] | ||
[[Category: Yamasaki | [[Category: Yamasaki N]] | ||
[[Category: Yao | [[Category: Yao M]] | ||
Latest revision as of 10:31, 30 October 2024
Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 2'-UMPCrystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 2'-UMP
Structural highlights
FunctionRNMC1_MOMCH Ribonuclease cleaving preferentially the 5'-side of uridine.[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedRibonuclease MC1 (RNase MC1) isolated from seeds of bitter gourd (Momordica charantia) consists of 190 amino acids and is characterized by a preferential cleavage at the 5'-side of uridine. This uridine specificity distinguishes RNase MC1 from other enzymes belonging to the RNase T2 family. The three-dimensional structures of RNase MC1, in a complex with either 2'-UMP or 3'-UMP, were determined at 1.48 and 1.77 A resolutions, respectively. The side chains of Gln9 and Asn71 interact with O4 and N3, respectively, of the uracil base by hydrogen bondings. In addition, the uracil base is sandwiched by the hydrophobic side chains of Leu73 and Phe80. Compared with these amino acid residues and corresponding residues in RNases in the RNase T2 family, Gln9 and Phe80 are highly conserved in the RNases in T2 family, while Asn71 and Leu73 in RNase MC1 are variant in sequences. It is thus likely that interactions of the side chains of Asn71 and Leu73 with the uracil base are responsible for the absolute uridine specificity of RNase MC1. Site-directed mutagenesis experiments showed that replacement of Asn by Thr decreased both the catalytic efficiency and the binding affinity by 2.3- and 7.0-fold, respectively, and substitution of Leu73 for Ala predominantly decreased the binding affinity by 14. 5-fold, compared with findings in case of wild-type RNase MC1. It is thus demonstrated that Asn71 and Leu73 play an essential role in uridine preference for RNase MC1. Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity.,Suzuki A, Yao M, Tanaka I, Numata T, Kikukawa S, Yamasaki N, Kimura M Biochem Biophys Res Commun. 2000 Aug 28;275(2):572-6. PMID:10964705[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||