1abr

From Proteopedia

(Difference between revisions)

Current revision

CRYSTAL STRUCTURE OF ABRIN-A

Structural highlights

1abr is a 2 chain structure with sequence from Abrus precatorius. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.14Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ABRA_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. Abrin-a is more toxic than ricin. The B chain is a galactose-specific lectin that facilitates the binding of abrin to the cell membrane that precedes endocytosis.

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

The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2.14 A to a R-factor of 18.9%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.013 A and 1.82 degrees, respectively. The overall protein folding is similar to that of ricin, but there are differences in the secondary structure, mostly of the A-chain. Several parts of the molecular surface differ significantly; some of them are quite near the active site cleft, and probably influence ribosome recognition. The positions of invariant active site residues remain the same, except the position of Tyr74. Two water molecules of hydrogen-bonded active site residues have been located in the active site cleft. Both of them may be responsible for hydrolyzing the N-C glycosidic bond. The current abrin-a structure is lactose free; this is probably essential for abrin-a crystallization. The B-chain is a glycoprotein, and the positions of several sugar residues of two sugar chains linked to earlier predicted glycosylation sites were determined. One of the sugar chains is a bridge between two neighboring molecules, since one of its mannose residues is connected to the galactose binding site of the neighboring molecule. Another sugar chain covers the surface of the B-chain.

Crystal structure of abrin-a at 2.14 A.,Tahirov TH, Lu TH, Liaw YC, Chen YL, Lin JY J Mol Biol. 1995 Jul 14;250(3):354-67. PMID:7608980^[1]

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

References

↑ Tahirov TH, Lu TH, Liaw YC, Chen YL, Lin JY. Crystal structure of abrin-a at 2.14 A. J Mol Biol. 1995 Jul 14;250(3):354-67. PMID:7608980 doi:http://dx.doi.org/10.1006/jmbi.1995.0382

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/1abr"

@@ Line 3: / Line 3: @@
 <StructureSection load='1abr' size='340' side='right'caption='[[1abr]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1abr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Abrpr Abrpr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ABR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ABR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1abr]] is a 2 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=1ABR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ABR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 2.14&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NGZ:2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE'>NGZ</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene>, <scene name='pdbligand=NGZ:2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE'>NGZ</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=1abr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1abr OCA], [https://pdbe.org/1abr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1abr RCSB], [https://www.ebi.ac.uk/pdbsum/1abr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1abr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/ABRA_ABRPR ABRA_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. Abrin-a is more toxic than ricin.  The B chain is a galactose-specific lectin that facilitates the binding of abrin to the cell membrane that precedes endocytosis.
+[https://www.uniprot.org/uniprot/ABRA_ABRPR ABRA_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. Abrin-a is more toxic than ricin.  The B chain is a galactose-specific lectin that facilitates the binding of abrin to the cell membrane that precedes endocytosis.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ab/1abr_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>
   </jmolCheckbox>
@@ Line 37: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Abrpr]]
+[[Category: Abrus precatorius]]
 [[Category: Large Structures]]
-[[Category: Chu, S C]]
+[[Category: Chu S-C]]
-[[Category: Liaw, Y C]]
+[[Category: Liaw Y-C]]
-[[Category: Lin, J Y]]
+[[Category: Lin J-Y]]
-[[Category: Lu, T H]]
+[[Category: Lu T-H]]
-[[Category: Tahirov, T H]]
+[[Category: Tahirov TH]]
-[[Category: Glycoprotein]]
-[[Category: Glycosidase-carbohydrate complex]]
-[[Category: Lectin]]
-[[Category: Plant seed protein]]
-[[Category: Plant toxin]]
-[[Category: Protein synthesis inhibitor]]
-[[Category: Toxin]]

1abr

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF ABRIN-A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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