This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2q3n

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:48, 9 March 2022

Agglutinin from Abrus Precatorius (APA-I)

Structural highlights

2q3n is a 2 chain structure with sequence from Abrus precatorius. This structure supersedes the now removed PDB entry 2amz. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Activity:	rRNA N-glycosylase, with EC number 3.2.2.22
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[AGGL_ABRPR] The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA (By similarity). Less toxic than abrin-a.^[1] [UniProtKB:P28590] The B chain is a galactose-specific lectin that facilitates the binding to the cell membrane that precedes endocytosis (By similarity).^[2] [UniProtKB:P28590]

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

Abrin and agglutinin-I from the seeds of Abrus precatorius are type II ribosome-inactivating proteins that inhibit protein synthesis in eukaryotic cells. The two toxins share a high degree of sequence similarity; however, agglutinin-I is weaker in its activity. We compared the kinetics of protein synthesis inhibition by abrin and agglutinin-I in two different cell lines and found that approximately 200-2000-fold higher concentration of agglutinin-I is needed for the same degree of inhibition. Like abrin, agglutinin-I also induced apoptosis in the cells by triggering the intrinsic mitochondrial pathway, although at higher concentrations as compared with abrin. The reason for the decreased toxicity of agglutinin-I became apparent on the analysis of the crystal structure of agglutinin-I obtained by us in comparison with that of the reported structure of abrin. The overall protein folding of agglutinin-I is similar to that of abrin-a with a single disulfide bond holding the toxic A subunit and the lectin-like B-subunit together, constituting a heterodimer. However, there are significant differences in the secondary structural elements, mostly in the A chain. The substitution of Asn-200 in abrin-a with Pro-199 in agglutinin-I seems to be a major cause for the decreased toxicity of agglutinin-I. This perhaps is not a consequence of any kink formation by a proline residue in the helical segment, as reported by others earlier, but due to fewer interactions that proline can possibly have with the bound substrate.

Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin.,Bagaria A, Surendranath K, Ramagopal UA, Ramakumar S, Karande AA J Biol Chem. 2006 Nov 10;281(45):34465-74. Epub 2006 Jun 13. PMID:16772301^[3]

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

References

↑ Liu CL, Tsai CC, Lin SC, Wang LI, Hsu CI, Hwang MJ, Lin JY. Primary structure and function analysis of the Abrus precatorius agglutinin A chain by site-directed mutagenesis. Pro(199) Of amphiphilic alpha-helix H impairs protein synthesis inhibitory activity. J Biol Chem. 2000 Jan 21;275(3):1897-901. PMID:10636890
↑ Liu CL, Tsai CC, Lin SC, Wang LI, Hsu CI, Hwang MJ, Lin JY. Primary structure and function analysis of the Abrus precatorius agglutinin A chain by site-directed mutagenesis. Pro(199) Of amphiphilic alpha-helix H impairs protein synthesis inhibitory activity. J Biol Chem. 2000 Jan 21;275(3):1897-901. PMID:10636890
↑ Bagaria A, Surendranath K, Ramagopal UA, Ramakumar S, Karande AA. Structure-function analysis and insights into the reduced toxicity of Abrus precatorius agglutinin I in relation to abrin. J Biol Chem. 2006 Nov 10;281(45):34465-74. Epub 2006 Jun 13. PMID:16772301 doi:http://dx.doi.org/10.1074/jbc.M601777200

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/2q3n"

@@ Line 3: / Line 3: @@
 <StructureSection load='2q3n' size='340' side='right'caption='[[2q3n]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q3n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Abrus_precatorius Abrus precatorius]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2amz 2amz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Q3N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q3n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Abrus_precatorius Abrus precatorius]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2amz 2amz]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3N FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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='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'>[http://proteopedia.org/fgij/fg.htm?mol=2q3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3n OCA], [http://pdbe.org/2q3n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q3n RCSB], [http://www.ebi.ac.uk/pdbsum/2q3n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3n 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=2q3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3n OCA], [https://pdbe.org/2q3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3n RCSB], [https://www.ebi.ac.uk/pdbsum/2q3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AGGL_ABRPR AGGL_ABRPR]] The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA (By similarity). Less toxic than abrin-a.<ref>PMID:10636890</ref> [UniProtKB:P28590]  The B chain is a galactose-specific lectin that facilitates the binding to the cell membrane that precedes endocytosis (By similarity).<ref>PMID:10636890</ref> [UniProtKB:P28590]
+[[https://www.uniprot.org/uniprot/AGGL_ABRPR AGGL_ABRPR]] The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA (By similarity). Less toxic than abrin-a.<ref>PMID:10636890</ref> [UniProtKB:P28590]  The B chain is a galactose-specific lectin that facilitates the binding to the cell membrane that precedes endocytosis (By similarity).<ref>PMID:10636890</ref> [UniProtKB:P28590]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2q3n

From Proteopedia

Revision as of 07:48, 9 March 2022

Agglutinin from Abrus Precatorius (APA-I)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox