1r4y

From Proteopedia

(Difference between revisions)

Current revision

SOLUTION STRUCTURE OF THE DELETION MUTANT DELTA(7-22) OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN

Structural highlights

1r4y is a 1 chain structure with sequence from Aspergillus giganteus. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 25 models
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNAS_ASPGI Alpha-sarcin is specific for purines in both single- and double-stranded RNA. Its toxic action on eukaryotic cells is the result of cleavage of a single phosphodiester bond in the 60S subunit of ribosomes.

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 deletion mutant Delta(7-22) of alpha-sarcin, unlike its wild-type protein counterpart, lacks the specific ability to degrade rRNA in intact ribosomes and exhibits an increased unspecific ribonuclease activity and decreased interaction with lipid vesicles. In trying to shed light on these differences, we report here on the three-dimensional structure of the Delta(7-22) alpha-sarcin mutant using NMR methods. We also evaluated its dynamic properties on the basis of theoretical models and measured its correlation time (6.2 nsec) by time-resolved fluorescence anisotropy. The global fold characteristic of ribotoxins is preserved in the mutant. The most significant differences with respect to the alpha-sarcin structure are concentrated in (1) loop 2, (2) loop 3, which adopts a new orientation, and (3) loop 5, which shows multiple conformations and an altered dynamics. The interactions between loop 5 and the N-terminal hairpin are lost in the mutant, producing increased solvent accessibility of the active-site residues. The degree of solvent exposure of the catalytic His 137 is similar to that shown by His 92 in RNase T1. Additionally, the calculated order parameters of residues belonging to loop 5 in the mutant correspond to an internal dynamic behavior more similar to RNase T1 than alpha-sarcin. On the other hand, changes in the relative orientation of loop 3 move the lysine-rich region 111-114, crucial for substrate recognition, away from the active site. All of the structural and dynamic data presented here reveal that the mutant is a hybrid of ribotoxins and noncytotoxic ribonucleases, consistent with its biological properties.

NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity.,Garcia-Mayoral MF, Garcia-Ortega L, Lillo MP, Santoro J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M Protein Sci. 2004 Apr;13(4):1000-11. PMID:15044731^[1]

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

References

↑ Garcia-Mayoral MF, Garcia-Ortega L, Lillo MP, Santoro J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M. NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity. Protein Sci. 2004 Apr;13(4):1000-11. PMID:15044731 doi:10.1110/ps.03532204

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/1r4y"

@@ Line 1: / Line 1: @@
 ==SOLUTION STRUCTURE OF THE DELETION MUTANT DELTA(7-22) OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN==
-<StructureSection load='1r4y' size='340' side='right'caption='[[1r4y]], [[NMR_Ensembles_of_Models | 25 NMR models]]' scene=''>
+<StructureSection load='1r4y' size='340' side='right'caption='[[1r4y]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r4y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspgi Aspgi]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R4Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r4y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_giganteus Aspergillus giganteus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R4Y FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1de3|1de3]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 25 models</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SAR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5060 ASPGI])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/rRNA_endonuclease rRNA endonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.10 3.1.27.10] </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=1r4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r4y OCA], [https://pdbe.org/1r4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r4y RCSB], [https://www.ebi.ac.uk/pdbsum/1r4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r4y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNAS_ASPGI RNAS_ASPGI]] Alpha-sarcin is specific for purines in both single- and double-stranded RNA. Its toxic action on eukaryotic cells is the result of cleavage of a single phosphodiester bond in the 60S subunit of ribosomes.
+[https://www.uniprot.org/uniprot/RNAS_ASPGI RNAS_ASPGI] Alpha-sarcin is specific for purines in both single- and double-stranded RNA. Its toxic action on eukaryotic cells is the result of cleavage of a single phosphodiester bond in the 60S subunit of ribosomes.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 16: / Line 14: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r4/1r4y_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 35: @@
 __TOC__
 </StructureSection>
-[[Category: Aspgi]]
+[[Category: Aspergillus giganteus]]
 [[Category: Large Structures]]
-[[Category: RRNA endonuclease]]
+[[Category: Bruix M]]
-[[Category: Bruix, M]]
+[[Category: Garcia-Mayoral MF]]
-[[Category: Garcia-Mayoral, M F]]
+[[Category: Garcia-Ortega L]]
-[[Category: Garcia-Ortega, L]]
+[[Category: Gavilanes JG]]
-[[Category: Gavilanes, J G]]
+[[Category: Lillo MP]]
-[[Category: Lillo, M P]]
+[[Category: Martinez Del Pozo A]]
-[[Category: Pozo, A Martinez Del]]
+[[Category: Rico M]]
-[[Category: Rico, M]]
+[[Category: Santoro J]]
-[[Category: Santoro, J]]
-[[Category: Alpha-beta protein]]
-[[Category: Hydrolase]]

1r4y

From Proteopedia

Current revision

SOLUTION STRUCTURE OF THE DELETION MUTANT DELTA(7-22) OF THE CYTOTOXIC RIBONUCLEASE ALPHA-SARCIN

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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