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[[Image:3rl9.png|left|200px]]


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==Crystal Structure of the complex of type I RIP with the hydrolyzed product of dATP, adenine at 1.9 A resolution==
The line below this paragraph, containing "STRUCTURE_3rl9", creates the "Structure Box" on the page.
<StructureSection load='3rl9' size='340' side='right'caption='[[3rl9]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3rl9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Momordica_balsamina Momordica balsamina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RL9 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
{{STRUCTURE_3rl9|  PDB=3rl9  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rl9 OCA], [https://pdbe.org/3rl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rl9 RCSB], [https://www.ebi.ac.uk/pdbsum/3rl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rl9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/D9J2T9_MOMBA D9J2T9_MOMBA]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The ribosome inactivating proteins (RIPs) of type 1 are plant toxins that eliminate adenine base selectively from the single stranded loop of rRNA. We report six crystal structures, type 1 RIP from Momordica balsamina (A), three in complexed states with ribose (B), guanine (C) and adenine (D) and two structures of MbRIP-1 when crystallized with adenosine triphosphate (ATP) (E) and 2'-deoxyadenosine triphosphate (2'-dATP) (F). These were determined at 1.67A, 1.60A, 2.20A, 1.70A, 2.07A and 1.90A resolutions respectively. The structures contained, (A) unbound protein molecule, (B) one protein molecule and one ribose sugar, (C) one protein molecule and one guanine base, (D) one protein molecule and one adenine base, (E) one protein molecule and one ATP-product adenine molecule and (F) one protein molecule and one 2'-dATP-product adenine molecule. Three distinct conformations of the side chain of Tyr70 were observed with (i) chi(1)=-66 degrees and chi(2)=165 degrees in structures (A) and (B); (ii) chi(1)=-95 degrees and chi(2)=70 degrees in structures (C), (D) and (E); and (iii) chi(1)=-163 degrees and chi(2)=87 degrees in structure (F). The conformation of Tyr70 in (F) corresponds to the structure of a conformational intermediate. This is the first structure which demonstrates that the slow conversion of DNA substrates by RIPs can be trapped during crystallization.


===Crystal Structure of the complex of type I RIP with the hydrolyzed product of dATP, adenine at 1.9 A resolution===
Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states.,Kushwaha GS, Pandey N, Sinha M, Singh SB, Kaur P, Sharma S, Singh TP Biochim Biophys Acta. 2012 Apr;1824(4):679-91. Epub 2012 Feb 14. PMID:22361570<ref>PMID:22361570</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3rl9" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_22361570}}, adds the Publication Abstract to the page
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 22361570 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_22361570}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[3rl9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Momordica_balsamina Momordica balsamina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RL9 OCA].
 
==Reference==
<ref group="xtra">PMID:022361570</ref><references group="xtra"/>
[[Category: Momordica balsamina]]
[[Category: Momordica balsamina]]
[[Category: RRNA N-glycosylase]]
[[Category: Kaur P]]
[[Category: Kaur, P.]]
[[Category: Kushwaha GS]]
[[Category: Kushwaha, G S.]]
[[Category: Pandey N]]
[[Category: Pandey, N.]]
[[Category: Sharma S]]
[[Category: Sharma, S.]]
[[Category: Singh TP]]
[[Category: Singh, T P.]]
[[Category: Sinha M]]
[[Category: Sinha, M.]]
[[Category: 6-aminopurine]]
[[Category: Hydrolase]]
[[Category: Inactivation]]
[[Category: Plant protein]]
[[Category: Rip]]
[[Category: Rna n-glycosidase]]

Latest revision as of 20:18, 1 November 2023

Crystal Structure of the complex of type I RIP with the hydrolyzed product of dATP, adenine at 1.9 A resolutionCrystal Structure of the complex of type I RIP with the hydrolyzed product of dATP, adenine at 1.9 A resolution

Structural highlights

3rl9 is a 1 chain structure with sequence from Momordica balsamina. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D9J2T9_MOMBA

Publication Abstract from PubMed

The ribosome inactivating proteins (RIPs) of type 1 are plant toxins that eliminate adenine base selectively from the single stranded loop of rRNA. We report six crystal structures, type 1 RIP from Momordica balsamina (A), three in complexed states with ribose (B), guanine (C) and adenine (D) and two structures of MbRIP-1 when crystallized with adenosine triphosphate (ATP) (E) and 2'-deoxyadenosine triphosphate (2'-dATP) (F). These were determined at 1.67A, 1.60A, 2.20A, 1.70A, 2.07A and 1.90A resolutions respectively. The structures contained, (A) unbound protein molecule, (B) one protein molecule and one ribose sugar, (C) one protein molecule and one guanine base, (D) one protein molecule and one adenine base, (E) one protein molecule and one ATP-product adenine molecule and (F) one protein molecule and one 2'-dATP-product adenine molecule. Three distinct conformations of the side chain of Tyr70 were observed with (i) chi(1)=-66 degrees and chi(2)=165 degrees in structures (A) and (B); (ii) chi(1)=-95 degrees and chi(2)=70 degrees in structures (C), (D) and (E); and (iii) chi(1)=-163 degrees and chi(2)=87 degrees in structure (F). The conformation of Tyr70 in (F) corresponds to the structure of a conformational intermediate. This is the first structure which demonstrates that the slow conversion of DNA substrates by RIPs can be trapped during crystallization.

Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states.,Kushwaha GS, Pandey N, Sinha M, Singh SB, Kaur P, Sharma S, Singh TP Biochim Biophys Acta. 2012 Apr;1824(4):679-91. Epub 2012 Feb 14. PMID:22361570[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Kushwaha GS, Pandey N, Sinha M, Singh SB, Kaur P, Sharma S, Singh TP. Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states. Biochim Biophys Acta. 2012 Apr;1824(4):679-91. Epub 2012 Feb 14. PMID:22361570 doi:10.1016/j.bbapap.2012.02.005

3rl9, resolution 1.90Å

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