1ahb: Difference between revisions

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<StructureSection load='1ahb' size='340' side='right'caption='[[1ahb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='1ahb' size='340' side='right'caption='[[1ahb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ahb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Balsam_pear Balsam pear]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AHB FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ahb]] 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=1AHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AHB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMP:FORMYCIN-5-MONOPHOSPHATE'>FMP</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]] 2.2&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMP:FORMYCIN-5-MONOPHOSPHATE'>FMP</scene></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=1ahb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ahb OCA], [http://pdbe.org/1ahb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ahb RCSB], [http://www.ebi.ac.uk/pdbsum/1ahb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ahb 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=1ahb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ahb OCA], [https://pdbe.org/1ahb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ahb RCSB], [https://www.ebi.ac.uk/pdbsum/1ahb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ahb ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RIP1_MOMCH RIP1_MOMCH]
== 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=1ahb 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=1ahb ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:8075985<ref>PMID:8075985</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ahb" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribosome inactivating protein|Ribosome inactivating protein]]
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Balsam pear]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RRNA N-glycosylase]]
[[Category: Momordica charantia]]
[[Category: Dong, Y]]
[[Category: Dong Y]]
[[Category: Ren, J]]
[[Category: Ren J]]
[[Category: Stuart, D I]]
[[Category: Stuart DI]]
[[Category: Wang, Y]]
[[Category: Wang Y]]
[[Category: Glycosidase]]

Latest revision as of 09:30, 7 February 2024

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

Structural highlights

1ahb is a 1 chain structure with sequence from Momordica charantia. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIP1_MOMCH

Evolutionary Conservation

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

See Also

1ahb, resolution 2.20Å

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