1il5

From Proteopedia

(Difference between revisions)

Revision as of 08:35, 16 August 2023

STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE (DDP)

Structural highlights

1il5 is a 2 chain structure with sequence from Ricinus communis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RICI_RICCO Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).

Evolutionary Conservation

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

Publication Abstract from PubMed

Ribosome inhibiting proteins, RIPs, are a widespread family of toxic enzymes. Ricin is a plant toxin used as a poison and biological warfare agent; shiga toxin is a homologue expressed by pathogenic strains of E. coli. There is interest in creating effective antidote inhibitors to this class of enzymes. RIPs act by binding and hydrolyzing a specific adenine base from rRNA. Previous virtual screens revealed that pterins could bind in the specificity pocket of ricin and inhibit the enzyme. In this paper we explore a range of compounds that could serve as better platforms for inhibitor design. This establishes the importance of key hydrogen bond donors and acceptors for active-site complementarity. 8-Methyl-9-oxoguanine is a soluble compound that has the best inhibitory properties of any platform tested. The X-ray structure of this complex revealed that the inhibitor binds in an unexpected way that provides insight for future design. Several inhibitors of ricin were also shown to be inhibitors of shiga toxin, suggesting this program has the potential to develop effective antidotes to an important form of food poisoning.

Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition.,Miller DJ, Ravikumar K, Shen H, Suh JK, Kerwin SM, Robertus JD J Med Chem. 2002 Jan 3;45(1):90-8. PMID:11754581^[1]

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

References

↑ Miller DJ, Ravikumar K, Shen H, Suh JK, Kerwin SM, Robertus JD. Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition. J Med Chem. 2002 Jan 3;45(1):90-8. PMID:11754581

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1il5"

@@ Line 3: / Line 3: @@
 <StructureSection load='1il5' size='340' side='right'caption='[[1il5]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1il5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IL5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1il5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IL5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DDP:2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE'>DDP</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]] 2.8&#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;'>[[1rtc|1rtc]], [[1br6|1br6]], [[1br5|1br5]], [[1fmp|1fmp]], [[1il3|1il3]], [[1il4|1il4]], [[1il9|1il9]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DDP:2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE'>DDP</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=1il5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1il5 OCA], [https://pdbe.org/1il5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1il5 RCSB], [https://www.ebi.ac.uk/pdbsum/1il5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1il5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO]] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).
+[https://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Ricin|Ricin]]
+*[[Ricin 3D structures|Ricin 3D structures]]
 == References ==
 <references/>
@@ Line 38: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Ricinus communis]]
-[[Category: Kerwin, S M]]
+[[Category: Kerwin SM]]
-[[Category: Miller, D J]]
+[[Category: Miller DJ]]
-[[Category: Ravikumar, K]]
+[[Category: Ravikumar K]]
-[[Category: Robertus, J D]]
+[[Category: Robertus JD]]
-[[Category: Shen, H]]
+[[Category: Shen H]]
-[[Category: Suh, J K]]
+[[Category: Suh J-K]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Ribosome-inhibiting protein]]
-[[Category: Structure-based design]]
-[[Category: Toxin-inhibitor complex]]

1il5

From Proteopedia

Revision as of 08:35, 16 August 2023

STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE (DDP)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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