This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1aha

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:30, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1aha.jpg|left|200px]]<br /><applet load="1aha" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1aha, resolution 2.2&Aring;" />
 
-
'''THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN'''<br />
 
-
==Overview==
+
==THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN==
-
BACKGROUND: alpha-Momorcharin (alpha MMC) is a type I ribosome-inactivating protein. It inhibits protein synthesis by hydrolytically removing a specific adenine residue from a highly conserved, single-stranded loop of rRNA. RESULTS: Here we describe the determination and refinement of the crystal structures of alpha MMC in the native state and in complexes with the product, adenine, and a substrate analogue, formycin 5'-monophosphate (FMP) at high resolution. Both adenine and the base of FMP are tightly bound; the ribose of bound FMP adopts a strained, high-energy conformation, which may mimic the structure of the transition state. CONCLUSIONS: These structures indicate that residues Tyr70, Glu160 and Arg163 of alpha MMC are the most critical for catalysis. We propose that the strained conformation of the ribose in the target adenosine weakens the glycoside bond. Partial protonation mediated by Arg163 then facilitates N-glycoside bond cleavage, leading to the formation of an oxycarbonium ion intermediate which is stabilized by the negatively-charged Glu160. Tyr70 adopts subtly different conformations in the three structures implying that it may be important in substrate recognition and perhaps catalysis.
+
<StructureSection load='1aha' size='340' side='right'caption='[[1aha]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1aha]] 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=1AHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AHA 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]] 2.2&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=1aha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aha OCA], [https://pdbe.org/1aha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aha RCSB], [https://www.ebi.ac.uk/pdbsum/1aha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aha ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/RIP1_MOMCH RIP1_MOMCH]
 +
== 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/ah/1aha_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1aha ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1AHA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Momordica_charantia Momordica charantia] with <scene name='pdbligand=ADE:'>ADE</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHA OCA].
+
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
The N-glycosidase mechanism of ribosome-inactivating proteins implied by crystal structures of alpha-momorcharin., Ren J, Wang Y, Dong Y, Stuart DI, Structure. 1994 Jan 15;2(1):7-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8075985 8075985]
+
[[Category: Large Structures]]
[[Category: Momordica charantia]]
[[Category: Momordica charantia]]
-
[[Category: Single protein]]
+
[[Category: Dong Y]]
-
[[Category: rRNA N-glycosylase]]
+
[[Category: Ren J]]
-
[[Category: Dong, Y.]]
+
[[Category: Stuart DI]]
-
[[Category: Ren, J.]]
+
[[Category: Wang Y]]
-
[[Category: Stuart, D I.]]
+
-
[[Category: Wang, Y.]]
+
-
[[Category: ADE]]
+
-
[[Category: glycosidase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:44:30 2008''
+

Current revision

THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN

PDB ID 1aha

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/1aha"
Personal tools