1r5d: Difference between revisions

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[[Image:1r5d.jpg|left|200px]]


{{Structure
==X-ray structure of bovine seminal ribonuclease swapping dimer from a new crystal form==
|PDB= 1r5d |SIZE=350|CAPTION= <scene name='initialview01'>1r5d</scene>, resolution 2.5&Aring;
<StructureSection load='1r5d' size='340' side='right'caption='[[1r5d]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<table><tr><td colspan='2'>[[1r5d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R5D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R5D FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
|GENE=  
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r5d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r5d OCA], [https://pdbe.org/1r5d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r5d RCSB], [https://www.ebi.ac.uk/pdbsum/1r5d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r5d ProSAT]</span></td></tr>
}}
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNS_BOVIN RNS_BOVIN] This enzyme hydrolyzes both single- and double-stranded RNA.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r5/1r5d_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1r5d ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.


'''X-ray structure of bovine seminal ribonuclease swapping dimer from a new crystal form'''
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.,Merlino A, Vitagliano L, Sica F, Zagari A, Mazzarella L Biopolymers. 2004 Apr 15;73(6):689-95. PMID:15048772<ref>PMID:15048772</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1r5d" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
1R5D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R5D OCA].
__TOC__
 
</StructureSection>
==Reference==
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer., Merlino A, Vitagliano L, Sica F, Zagari A, Mazzarella L, Biopolymers. 2004 Apr 15;73(6):689-95. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15048772 15048772]
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Pancreatic ribonuclease]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Mazzarella L]]
[[Category: Mazzarella, L.]]
[[Category: Merlino A]]
[[Category: Merlino, A.]]
[[Category: Sica F]]
[[Category: Sica, F.]]
[[Category: Vitagliano L]]
[[Category: Vitagliano, L.]]
[[Category: Zagari A]]
[[Category: Zagari, A.]]
[[Category: 3d domain swapping]]
[[Category: ligand binding]]
[[Category: population shift]]
[[Category: protein dynamic]]
[[Category: protein structure-function]]
[[Category: ribonuclease]]
[[Category: x-ray diffraction]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:47:07 2008''

Latest revision as of 07:25, 9 October 2024

X-ray structure of bovine seminal ribonuclease swapping dimer from a new crystal form

1r5d, resolution 2.50Å

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