3hiv: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='3hiv' size='340' side='right'caption='[[3hiv]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
<StructureSection load='3hiv' size='340' side='right'caption='[[3hiv]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3hiv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Common_soapwort Common soapwort]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HIV FirstGlance]. <br>
<table><tr><td colspan='2'>[[3hiv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saponaria_officinalis Saponaria officinalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HIV FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TXN:(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-6,8-DIHYDRO-9H-PURIN-9-YL)-2-(HYDROXYMETHYL)-4-METHOXYTETRAHYDROFURAN-3-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]PYRROLIDIN-3-YL}OXY)(HYDROXY)PHOSPHORYL]OXY}METHYL)-4-METHOXYTETRAHYDROFURAN-3-YL+3-HYDROXYPROPYL+HYDROGEN+(S)-PHOSPHATE'>TXN</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]] 2.14&#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;'>[[3hio|3hio]], [[3hiq|3hiq]], [[3his|3his]], [[3hit|3hit]], [[3hiw|3hiw]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TXN:(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)-2-({[(S)-({(3R,4R)-4-({[(S)-{[(2R,3R,4R,5R)-5-(2-AMINO-6-OXO-6,8-DIHYDRO-9H-PURIN-9-YL)-2-(HYDROXYMETHYL)-4-METHOXYTETRAHYDROFURAN-3-YL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]PYRROLIDIN-3-YL}OXY)(HYDROXY)PHOSPHORYL]OXY}METHYL)-4-METHOXYTETRAHYDROFURAN-3-YL+3-HYDROXYPROPYL+HYDROGEN+(S)-PHOSPHATE'>TXN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] </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=3hiv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiv OCA], [https://pdbe.org/3hiv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hiv RCSB], [https://www.ebi.ac.uk/pdbsum/3hiv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hiv 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=3hiv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hiv OCA], [https://pdbe.org/3hiv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hiv RCSB], [https://www.ebi.ac.uk/pdbsum/3hiv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hiv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q2QEH4_SAPOF Q2QEH4_SAPOF]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 19: Line 20:
</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=3hiv 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=3hiv ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple pi-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the pi-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H(2)O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.
Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.,Ho MC, Sturm MB, Almo SC, Schramm VL Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20276-81. Epub 2009 Nov 17. PMID:19920175<ref>PMID:19920175</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3hiv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Common soapwort]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RRNA N-glycosylase]]
[[Category: Saponaria officinalis]]
[[Category: Almo, S C]]
[[Category: Almo SC]]
[[Category: Ho, M]]
[[Category: Ho M]]
[[Category: Schramm, V L]]
[[Category: Schramm VL]]
[[Category: Sturm, M B]]
[[Category: Sturm MB]]
[[Category: Hydrolase]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Plant defense]]
[[Category: Protein synthesis inhibitor]]
[[Category: Ribosome inactivating protein]]
[[Category: Rip]]
[[Category: Toxin]]
[[Category: Transition state]]

Latest revision as of 10:00, 21 February 2024

Crystal structure of Saporin-L1 in complex with the trinucleotide inhibitor, a transition state analogue

3hiv, resolution 2.14Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=3hiv&oldid=4065323"