|
|
| (2 intermediate revisions not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='2zr1' size='340' side='right'caption='[[2zr1]], [[Resolution|resolution]] 2.60Å' scene=''> | | <StructureSection load='2zr1' size='340' side='right'caption='[[2zr1]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zr1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Abrus_precatorius Abrus precatorius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZR1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZR1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zr1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Abrus_precatorius Abrus precatorius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZR1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZR1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</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]] 2.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2q3n|2q3n]], [[1abr|1abr]]</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zr1 OCA], [https://pdbe.org/2zr1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zr1 RCSB], [https://www.ebi.ac.uk/pdbsum/2zr1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zr1 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zr1 OCA], [http://pdbe.org/2zr1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zr1 RCSB], [http://www.ebi.ac.uk/pdbsum/2zr1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zr1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 16: |
Line 15: |
| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zr/2zr1_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zr/2zr1_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| Line 39: |
Line 38: |
| | [[Category: Abrus precatorius]] | | [[Category: Abrus precatorius]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: RRNA N-glycosylase]]
| + | [[Category: Cheng J]] |
| - | [[Category: Cheng, J]] | + | [[Category: Lin JY]] |
| - | [[Category: Lin, J Y]] | + | [[Category: Liu CL]] |
| - | [[Category: Liu, C L]] | + | [[Category: Lu TH]] |
| - | [[Category: Lu, T H]] | + | |
| - | [[Category: Agglutinin abrin]]
| + | |
| - | [[Category: Glycoprotein]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Immunotoxin]]
| + | |
| - | [[Category: Lectin]]
| + | |
| - | [[Category: Plant defense]]
| + | |
| - | [[Category: Plant protein]]
| + | |
| - | [[Category: Protein synthesis inhibitor]]
| + | |
| - | [[Category: Pyrrolidone carboxylic acid]]
| + | |
| - | [[Category: Ribosome-inactivating protein]]
| + | |
| - | [[Category: Toxin]]
| + | |
| Structural highlights
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
X-ray crystal structure determination of agglutinin from Abrus precatorius in Taiwan is presented. The crystal structure of agglutinin, a type II ribosome-inactivating protein (RIP) from the seeds of Abrus precatorius in Taiwan, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of abrin-a as the template. The structure has space group P4(1)2(1)2 with Z = 8, and been refined at 2.6 A to R-factor of 20.4%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.009 A and 1.3 degrees. Primary, secondary, tertiary and quaternary structures of agglutinin have been described and compared with those of abrin-a to a certain extent. In subsequent docking research, we found that Asn200 of abrin-a may form a critical hydrogen bond with G4323 of 28SRNA, while corresponding Pro199 of agglutinin is a kink hydrophobic residue bound with the cleft in a more compact complementary relationship. This may explain the lower toxicity of agglutinin than abrin-a, despite of similarity in secondary structure and the activity cleft of two RIPs.
A biophysical elucidation for less toxicity of agglutinin than abrin-a from the seeds of Abrus precatorius in consequence of crystal structure.,Cheng J, Lu TH, Liu CL, Lin JY J Biomed Sci. 2010 Apr 30;17:34. PMID:20433687[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
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
- ↑ Cheng J, Lu TH, Liu CL, Lin JY. A biophysical elucidation for less toxicity of agglutinin than abrin-a from the seeds of Abrus precatorius in consequence of crystal structure. J Biomed Sci. 2010 Apr 30;17:34. PMID:20433687 doi:10.1186/1423-0127-17-34
|
