1kab: Difference between revisions

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New page: left|200px<br /><applet load="1kab" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kab, resolution 1.8Å" /> '''STRESS AND STRAIN IN ...
 
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[[Image:1kab.jpg|left|200px]]<br /><applet load="1kab" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1kab, resolution 1.8&Aring;" />
'''STRESS AND STRAIN IN STAPHYLOCOCCAL NUCLEASE'''<br />


==Overview==
==STRESS AND STRAIN IN STAPHYLOCOCCAL NUCLEASE==
Protein molecules generally adopt a tertiary structure in which all, backbone and side chain conformations are arranged in local energy minima;, however, in several well-refined protein structures examples of locally, strained geometries, such as cis peptide bonds, have been observed., Staphylococcal nuclease A contains a single cis peptide bond between, residues Lys 116 and Pro 117 within a type VIa beta-turn. Alternative, native folded forms of nuclease A have been detected by NMR spectroscopy, and attributed to a mixture of cis and trans isomers at the Lys 116-Pro, 117 peptide bond. Analyses of nuclease variants K116G and K116A by NMR, spectroscopy and X-ray crystallography are reported herein. The structure, of K116A is indistinguishable from that of nuclease A, including a cis, 116-117 peptide bond (92% populated in solution). The overall fold of, K116G is also indistinguishable from nuclease A except in the region of, the substitution (residues 112-117), which contains a predominantly trans, Gly 116-Pro 117 peptide bond (80% populated in solution). Both Lys and Ala, would be prohibited from adopting the backbone conformation of Gly 116 due, to steric clashes between the beta-carbon and the surrounding residues., One explanation for these results is that the position of the ends of the, residue 112-117 loop only allow trans conformations where the local, backbone interactions associated with the phi and psi torsion angles are, strained. When the 116-117 peptide bond is cis, less strained backbone, conformations are available. Thus the relaxation of the backbone strain, intrinsic to the trans conformation compensates for the energetically, unfavorable cis X-Pro peptide bond. With the removal of the side chain, from residue 116 (K116G), the backbone strain of the trans conformation is, reduced to the point that the conformation associated with the cis peptide, bond is no longer favorable.
<StructureSection load='1kab' size='340' side='right'caption='[[1kab]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kab]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KAB FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</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=1kab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kab OCA], [https://pdbe.org/1kab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kab RCSB], [https://www.ebi.ac.uk/pdbsum/1kab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kab ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
== 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/ka/1kab_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1kab ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1KAB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Active as [http://en.wikipedia.org/wiki/Hydrolase Hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.33.1 3.1.33.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KAB OCA].
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Stress and strain in staphylococcal nuclease., Hodel A, Kautz RA, Jacobs MD, Fox RO, Protein Sci. 1993 May;2(5):838-50. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8495201 8495201]
[[Category: Large Structures]]
[[Category: Hydrolase]]
[[Category: Single protein]]
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
[[Category: Fox, R.O.]]
[[Category: Fox RO]]
[[Category: Hodel, A.]]
[[Category: Hodel A]]
[[Category: hydrolase(phosphoric diester)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:59:52 2007''

Latest revision as of 10:45, 7 February 2024

STRESS AND STRAIN IN STAPHYLOCOCCAL NUCLEASESTRESS AND STRAIN IN STAPHYLOCOCCAL NUCLEASE

Structural highlights

1kab is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NUC_STAAU Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1kab, resolution 1.80Å

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