1kdc: Difference between revisions

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New page: left|200px<br /><applet load="1kdc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kdc, resolution 2.0Å" /> '''STABILIZATION OF A ST...
 
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[[Image:1kdc.jpg|left|200px]]<br /><applet load="1kdc" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1kdc, resolution 2.0&Aring;" />
'''STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING'''<br />


==Overview==
==STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING==
Staphylococcal nuclease is found in two folded conformations that differ, in the isomerization of the Lys 116-Pro 117 peptide bond, resulting in two, different conformations of the residue 112-117 loop. The cis form is, favored over the trans with an occupancy of 90%. Previous mutagenesis, studies have shown that when Lys 116 is replaced by glycine, a trans, conformation is stabilized relative to the cis conformation by the release, of steric strain in the trans form. However, when Lys 116 is replaced with, alanine, the resulting variant protein is identical to the wild-type, protein in its structure and in the dominance of the cis configuration., The results of these studies suggested that any nuclease variant with a, non-glycine residue at position 116 should also favor the cis form because, of steric requirements of the beta-carbon at this position. In this, report, we present a structural analysis of four nuclease variants with, substitutions at position 116. Two variants, K116E and K116M, follow the, "beta-carbon" hypothesis by favoring the cis form. Furthermore, the, crystal structure of K116E is nearly identical to that of the wild-type, protein. Two additional variants, K116D and K116N, provide exceptions to, this simple "beta-carbon" rule in that the trans conformation is, stabilized relative to the cis configuration by these substitutions., Crystallographic data indicate that this stabilization is effected through, the addition of tertiary interactions between the side chain of position, 116 with the surrounding protein and water structure. The detailed trans, conformation of the K116D variant appears to be similar to the trans, conformation observed in the K116G variant, suggesting that these two, mutations stabilize the same conformation but through different, mechanisms.
<StructureSection load='1kdc' size='340' side='right'caption='[[1kdc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kdc]] 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=1KDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KDC 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]] 2&#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=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [https://pdbe.org/1kdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [https://www.ebi.ac.uk/pdbsum/1kdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdc 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/kd/1kdc_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=1kdc ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1KDC 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/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KDC OCA].
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Stabilization of a strained protein loop conformation through protein engineering., Hodel A, Kautz RA, Fox RO, Protein Sci. 1995 Mar;4(3):484-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7795531 7795531]
[[Category: Large Structures]]
[[Category: Micrococcal nuclease]]
[[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 19:04:52 2007''

Latest revision as of 10:46, 7 February 2024

STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERINGSTABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING

Structural highlights

1kdc 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 2Å
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

1kdc, resolution 2.00Å

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