1qci: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1qci]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytolacca_americana Phytolacca americana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QCI FirstGlance]. <br>
<table><tr><td colspan='2'>[[1qci]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytolacca_americana Phytolacca americana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QCI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QCI FirstGlance]. <br>
</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>
</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&#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;'>[[1qcg|1qcg]], [[1qcj|1qcj]]</div></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=1qci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qci OCA], [https://pdbe.org/1qci PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qci RCSB], [https://www.ebi.ac.uk/pdbsum/1qci PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qci 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=1qci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qci OCA], [https://pdbe.org/1qci PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qci RCSB], [https://www.ebi.ac.uk/pdbsum/1qci PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qci ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RIP1_PHYAM RIP1_PHYAM]] Inhibits viral infection of plants, and protein synthesis in vitro.  
[https://www.uniprot.org/uniprot/RIP1_PHYAM RIP1_PHYAM] Inhibits viral infection of plants, and protein synthesis in vitro.
== 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=1qci 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=1qci ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The pokeweed antiviral protein (PAP) belongs to a family of ribosome-inactivating proteins (RIP), which depurinate ribosomal RNA through their site-specific N-glycosidase activity. We report low temperature, three-dimensional structures of PAP co-crystallized with adenyl-guanosine (ApG) and adenyl-cytosine-cytosine (ApCpC). Crystal structures of 2.0-2.1 A resolution revealed that both ApG or ApCpC nucleotides are cleaved by PAP, leaving only the adenine base clearly visible in the active site pocket of PAP. ApCpC does not resemble any known natural substrate for any ribosome-inactivating proteins and its cleavage by PAP provides unprecedented evidence for a broad spectrum N-glycosidase activity of PAP toward adenine-containing single stranded RNA. We also report the analysis of a 2.1 A crystal structure of PAP complexed with the RIP inhibitor pteoric acid. The pterin ring is strongly bound in the active site, forming four hydrogen bonds with active site residues and one hydrogen bond with the coordinated water molecule. The second 180 degrees rotation conformation of pterin ring can form only three hydrogen bonds in the active site and is less energetically favorable. The benzoate moiety is parallel to the protein surface of PAP and forms only one hydrogen bond with the guanido group of Arg135.
X-ray crystallographic analysis of the structural basis for the interactions of pokeweed antiviral protein with its active site inhibitor and ribosomal RNA substrate analogs.,Kurinov IV, Myers DE, Irvin JD, Uckun FM Protein Sci. 1999 Sep;8(9):1765-72. PMID:10493577<ref>PMID:10493577</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1qci" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribosome inactivating protein|Ribosome inactivating protein]]
*[[Ribosome inactivating protein|Ribosome inactivating protein]]
== References ==
*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Phytolacca americana]]
[[Category: Phytolacca americana]]
[[Category: Irvin, J D]]
[[Category: Irvin JD]]
[[Category: Kurinov, I V]]
[[Category: Kurinov IV]]
[[Category: Myers, D E]]
[[Category: Myers DE]]
[[Category: Uckun, F M]]
[[Category: Uckun FM]]
[[Category: Antiviral protein]]
[[Category: Pokeweed antiviral protein]]
[[Category: Ribosome inactivating protein]]
[[Category: Rna substrate analog]]

Revision as of 09:03, 17 April 2024

LOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH ADENINELOW TEMPERATURE STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH ADENINE

Structural highlights

1qci is a 2 chain structure with sequence from Phytolacca americana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIP1_PHYAM Inhibits viral infection of plants, and protein synthesis in vitro.

Evolutionary Conservation

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

See Also

1qci, resolution 2.00Å

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