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1kab

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[[Image:1kab.jpg|left|200px]]
 
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{{Structure
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==STRESS AND STRAIN IN STAPHYLOCOCCAL NUCLEASE==
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|PDB= 1kab |SIZE=350|CAPTION= <scene name='initialview01'>1kab</scene>, resolution 1.8&Aring;
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<StructureSection load='1kab' size='340' side='right'caption='[[1kab]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<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>
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|ACTIVITY= <span class='plainlinks'>[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] </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]] 1.8&#8491;</td></tr>
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|GENE=
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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=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>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Function ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kab OCA], [http://www.ebi.ac.uk/pdbsum/1kab PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kab RCSB]</span>
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[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.
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}}
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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/ka/1kab_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=1kab ConSurf].
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<div style="clear:both"></div>
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'''STRESS AND STRAIN IN STAPHYLOCOCCAL NUCLEASE'''
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==See Also==
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*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Large Structures]]
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==About this Structure==
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1KAB is a [[Single protein]] structure of sequence from [http://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].
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==Reference==
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Stress and strain in staphylococcal nuclease., Hodel A, Kautz RA, Jacobs MD, Fox RO, Protein Sci. 1993 May;2(5):838-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8495201 8495201]
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[[Category: Hydrolase]]
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[[Category: Single protein]]
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[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
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[[Category: Fox, R O.]]
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[[Category: Fox RO]]
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[[Category: Hodel, A.]]
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[[Category: Hodel A]]
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[[Category: hydrolase(phosphoric diester)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:45:38 2008''
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Current revision

STRESS AND STRAIN IN STAPHYLOCOCCAL NUCLEASE

PDB ID 1kab

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