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1rbe

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[[Image:1rbe.gif|left|200px]]
 
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{{Structure
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==CRYSTALLOGRAPHIC STRUCTURES OF RIBONUCLEASE S VARIANTS WITH NONPOLAR SUBSTITUTION AT POSITION 13: PACKING AND CAVITIES==
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|PDB= 1rbe |SIZE=350|CAPTION= <scene name='initialview01'>1rbe</scene>, resolution 1.75&Aring;
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<StructureSection load='1rbe' size='340' side='right'caption='[[1rbe]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1rbe]] 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=1RBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RBE FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rbe OCA], [https://pdbe.org/1rbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rbe RCSB], [https://www.ebi.ac.uk/pdbsum/1rbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rbe ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rbe OCA], [http://www.ebi.ac.uk/pdbsum/1rbe PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rbe RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/1rbe_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1rbe ConSurf].
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<div style="clear:both"></div>
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'''CRYSTALLOGRAPHIC STRUCTURES OF RIBONUCLEASE S VARIANTS WITH NONPOLAR SUBSTITUTION AT POSITION 13: PACKING AND CAVITIES'''
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==See Also==
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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==Overview==
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<references/>
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Seven hydrophobic residues ranging in size from glycine to phenylalanine have been substituted for the wild-type methionine residue at position 13 in a 15-residue truncated version (S15) of S-peptide, the small component of ribonuclease S. Complexes of both S-15 and the seven variants with S-protein yielded isomorphous crystals. The structures of all eight complexes have been refined to final R-factors in the range of 17-19%. [See Kim, E. E. Varadarajan, R., Wyckoff, H. W., and Richards, F. M. (1992) Biochemistry (preceding paper in this issue) for the description of the reference S-15 complex.] Multiple side-chain conformations were seen for six residues in all of the complexes and for two to three additional residues in at least some of the complexes. Three of the complexes, Gly, Ala, and alpha-amino-n-butyric acid (ANB), contained a single water molecule in the cavity near residue 13 that makes three hydrogen bonds to protein atoms. Although space is available, no evidence for additional water in this region, ordered or disordered, was found. The atoms in the cavity wall tend to shrink the cavity by moving in on the small residues and to swell the cavity by moving out for the larger Phe substitution. A swelling seen with leucine was attributed to a shape effect since Leu, Ile, and Met all have the same volume. A slight volume contraction of the collection of interior residues outside of the region of position 13 was also noted. (All changes noted are in the direction to maintain a constant packing density averaged over the whole protein.) Leu51, a surface hydrophobic residue, moved considerably in the G, A, and ANB complexes in directionswhich would tend to decrease the cavity volume. The only other major change in position, 1.5 A, was the 66-69 loop, which is about 25 A from position 13. His12, Phe120, and Asp121 appear to be involved in this movement, but the connection with position 13 is not clear at all. The thermodynamic data on the association reaction for all of these complexes have been previously reported [Connelly, P. R., Varadarajan, R., Sturtevant, J. M., &amp; Richards, F. M. (1990) Biochemistry 29, 6108-6114; Varadarajan, R., Connelly, P. R., Sturtevant, J. M., &amp; Richards, F. M. (1992) Biochemistry 31, 1421-1426]. Some comments are offered on our initial attempts to correlate the structural changes with the changes in the thermodynamic parameters.(ABSTRACT TRUNCATED AT 400 WORDS)
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__TOC__
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</StructureSection>
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==About this Structure==
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1RBE is a [[Protein complex]] structure of sequences 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=1RBE OCA].
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==Reference==
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Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities., Varadarajan R, Richards FM, Biochemistry. 1992 Dec 15;31(49):12315-27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1463720 1463720]
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[[Category: Bos taurus]]
[[Category: Bos taurus]]
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[[Category: Pancreatic ribonuclease]]
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[[Category: Large Structures]]
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[[Category: Protein complex]]
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[[Category: Richards FM]]
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[[Category: Richards, F M.]]
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[[Category: Varadarajan R]]
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[[Category: Varadarajan, R.]]
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[[Category: hydrolase(phosphoric diester,rna)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:25:49 2008''
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Current revision

CRYSTALLOGRAPHIC STRUCTURES OF RIBONUCLEASE S VARIANTS WITH NONPOLAR SUBSTITUTION AT POSITION 13: PACKING AND CAVITIES

PDB ID 1rbe

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