1kdc - Revision history

OCA at 07:46, 7 February 2024

2024-02-07T07:46:06Z

←Older revision		Revision as of 07:46, 7 February 2024
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	<StructureSection load='1kdc' size='340' side='right'caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kdc' size='340' side='right'caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. 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>	+	<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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>~~[https://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1~~] ~~</span>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</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>		<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>		</table>
	== Function ==		== 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.	+	[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=1kdc ConSurf].		</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>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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:7795531<ref>PMID:7795531</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kdc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]		*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Micrococcal nuclease~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: Fox~~, R O~~]]	+	[[Category: Fox RO]]
-	[[Category: Hodel, A]]	+	[[Category: Hodel A]]

OCA at 06:52, 11 August 2021

2021-08-11T06:52:28Z

←Older revision		Revision as of 06:52, 11 August 2021
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	<StructureSection load='1kdc' size='340' side='right'caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kdc' size='340' side='right'caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. 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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. 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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~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] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [~~http~~://pdbe.org/1kdc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kdc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdc ProSAT]</span></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>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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.	+	[[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]	+	*[[Staphylococcal nuclease 3D structures\|Staphylococcal nuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:11, 6 November 2019

2019-11-06T09:11:36Z

←Older revision		Revision as of 09:11, 6 November 2019
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	==STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING==		==STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING==
-	<StructureSection load='1kdc' size='340' side='right' caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1kdc' size='340' side='right'caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1kdc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kdc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Fox, R O]]		[[Category: Fox, R O]]
	[[Category: Hodel, A]]		[[Category: Hodel, A]]

OCA at 21:22, 24 January 2018

2018-01-24T21:22:03Z

←Older revision		Revision as of 21:22, 24 January 2018
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		+
	==STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING==		==STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING==
	<StructureSection load='1kdc' size='340' side='right' caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kdc' size='340' side='right' caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [http://pdbe.org/1kdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [http://www.ebi.ac.uk/pdbsum/1kdc PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [http://pdbe.org/1kdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [http://www.ebi.ac.uk/pdbsum/1kdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kdc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/1kdc_consurf.spt"</scriptWhenChecked>	+	<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>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 1kdc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kdc" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:06, 8 February 2016

2016-02-08T11:06:42Z

←Older revision		Revision as of 11:06, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:54, 10 September 2015

2015-09-10T10:54:38Z

←Older revision		Revision as of 10:54, 10 September 2015
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	<StructureSection load='1kdc' size='340' side='right' caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1kdc' size='340' side='right' caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with 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=1KDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [http://www.ebi.ac.uk/pdbsum/1kdc PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [http://pdbe.org/1kdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [http://www.ebi.ac.uk/pdbsum/1kdc PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1kdc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
-	[[Category: Staphylococcus aureus]]
	[[Category: Fox, R O]]		[[Category: Fox, R O]]
	[[Category: Hodel, A]]		[[Category: Hodel, A]]

OCA at 22:52, 24 December 2014

2014-12-24T22:52:13Z

←Older revision		Revision as of 22:52, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with 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=1KDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with 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=1KDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [http://www.ebi.ac.uk/pdbsum/1kdc PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [http://www.ebi.ac.uk/pdbsum/1kdc PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
-	[[Category: Fox, R O.]]	+	[[Category: Fox, R O]]
-	[[Category: Hodel, A.]]	+	[[Category: Hodel, A]]

OCA at 09:18, 28 September 2014

2014-09-28T09:18:47Z

←Older revision		Revision as of 09:18, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1kdc.~~png\|left~~\|200px]]	+	==STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING==
		+	<StructureSection load='1kdc' size='340' side='right' caption='[[1kdc]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kdc]] is a 1 chain structure with 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=1KDC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KDC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kdc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kdc RCSB], [http://www.ebi.ac.uk/pdbsum/1kdc PDBsum]</span></td></tr>
		+	<table>
		+	== 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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_1kdc\| PDB=1kdc \| SCENE= }}~~	+	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:7795531<ref>PMID:7795531</ref>

-	~~===STABILIZATION OF A STRAINED PROTEIN LOOP CONFORMATION THROUGH PROTEIN ENGINEERING===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_7795531}}~~	+	==See Also==
-		+	*[[Staphylococcal nuclease\|Staphylococcal nuclease]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1kdc~~]] is a 1 chain structure with 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=1KDC OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:007795531<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Fox, R O.]]		[[Category: Fox, R O.]]
	[[Category: Hodel, A.]]		[[Category: Hodel, A.]]

OCA: Protected "1kdc" [edit=sysop:move=sysop]

2012-12-05T20:48:17Z

Protected "1kdc" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:48, 5 December 2012

OCA at 20:48, 5 December 2012

2012-12-05T20:48:13Z

←Older revision		Revision as of 20:48, 5 December 2012
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-	{{Seed}}
	[[Image:1kdc.png\|left\|200px]]		[[Image:1kdc.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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	{{STRUCTURE_1kdc\| PDB=1kdc \| SCENE= }}		{{STRUCTURE_1kdc\| PDB=1kdc \| SCENE= }}

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

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_7795531}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 7795531 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_7795531}}		{{ABSTRACT_PUBMED_7795531}}

	==About this Structure==		==About this Structure==
-	~~1KDC~~ is a 1 chain 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=1KDC OCA].	+	[[1kdc]] is a 1 chain structure with 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=1KDC OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~7795531~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007795531</ref><references group="xtra"/>
	[[Category: Micrococcal nuclease]]		[[Category: Micrococcal nuclease]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Fox, R O.]]		[[Category: Fox, R O.]]
	[[Category: Hodel, A.]]		[[Category: Hodel, A.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:31:56 2009''