3lpr - Revision history

OCA at 06:37, 14 October 2020

OCA — Wed, 14 Oct 2020 06:37:06 GMT

←Older revision		Revision as of 06:37, 14 October 2020
Line 1:		Line 1:

	==STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS==		==STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS==
-	<StructureSection load='3lpr' size='340' side='right' caption='[[3lpr]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='3lpr' size='340' side='right'caption='[[3lpr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29487 Atcc 29487]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LPR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29487 Atcc 29487]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3LPR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </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=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://pdbe.org/3lpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB], [http://www.ebi.ac.uk/pdbsum/3lpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lpr ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://pdbe.org/3lpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB], [http://www.ebi.ac.uk/pdbsum/3lpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lpr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Alpha-lytic protease\|Alpha-lytic protease]]	+	*[[Alpha-lytic protease 3D structures\|Alpha-lytic protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	[[Category: Alpha-lytic endopeptidase]]		[[Category: Alpha-lytic endopeptidase]]
	[[Category: Atcc 29487]]		[[Category: Atcc 29487]]
		+	[[Category: Large Structures]]
	[[Category: Agard, D A]]		[[Category: Agard, D A]]
	[[Category: Bone, R]]		[[Category: Bone, R]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Serine proteinase]]		[[Category: Serine proteinase]]

OCA at 06:55, 9 January 2019

OCA — Wed, 09 Jan 2019 06:55:39 GMT

←Older revision		Revision as of 06:55, 9 January 2019
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lp/3lpr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lp/3lpr_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>

OCA at 07:11, 11 August 2016

OCA — Thu, 11 Aug 2016 07:11:23 GMT

←Older revision		Revision as of 07:11, 11 August 2016
Line 1:		Line 1:
		+
	==STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS==		==STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS==
	<StructureSection load='3lpr' size='340' side='right' caption='[[3lpr]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3lpr' size='340' side='right' caption='[[3lpr]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Lysobacter_enzymogenes Lysobacter enzymogenes~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LPR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29487 Atcc 29487]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LPR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </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=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB], [http://www.ebi.ac.uk/pdbsum/3lpr 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=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://pdbe.org/3lpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB], [http://www.ebi.ac.uk/pdbsum/3lpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lpr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=3lpr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 3lpr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Alpha-lytic endopeptidase]]		[[Category: Alpha-lytic endopeptidase]]
-	[[Category: ~~Lysobacter enzymogenes~~]]	+	[[Category: Atcc 29487]]
	[[Category: Agard, D A]]		[[Category: Agard, D A]]
	[[Category: Bone, R]]		[[Category: Bone, R]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Serine proteinase]]		[[Category: Serine proteinase]]

OCA at 07:37, 20 January 2015

OCA — Tue, 20 Jan 2015 07:37:20 GMT

OCA at 10:48, 29 September 2014

OCA — Mon, 29 Sep 2014 10:48:13 GMT

←Older revision		Revision as of 10:48, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3lpr.~~png~~\|~~left~~\|200px]]	+	==STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS==
		+	<StructureSection load='3lpr' size='340' side='right' caption='[[3lpr]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LPR FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </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=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB], [http://www.ebi.ac.uk/pdbsum/3lpr 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/lp/3lpr_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 ==
		+	Binding pocket mutants of alpha-lytic protease (Met 192----Ala and Met 213----Ala) have been constructed recently in an effort to create a protease specific for Met just prior to the scissile bond. Instead, mutation resulted in proteases with extraordinarily broad specificity profiles and high activity [Bone, R., Silen, J. L., & Agard, D. A. (1989) Nature 339, 191-195]. To understand the structural basis for the unexpected specificity profiles of these mutants, high-resolution X-ray crystal structures have been determined for complexes of each mutant with a series of systematically varying peptidylboronic acids. These inhibitory analogues of high-energy reaction intermediates provide models for how substrates with different side chains interact with the enzyme during the transition state. Fifteen structures have been analyzed qualitatively and quantitatively with respect to enzyme-inhibitor hydrogen-bond lengths, buried hydrophobic surface area, unfilled cavity volume, and the magnitude of inhibitor accommodating conformational adjustments (particularly in the region of another binding pocket residue, Val 217A). Comparison of these four parameters with the Ki of each inhibitor and the kcat and Km of the analogous substrates indicates that while no single structural parameter consistently correlates with activity or inhibition, the observed data can be understood as a combination of effects. Furthermore, the relative contribution of each term differs for the three enzymes, reflecting the altered conformational energetics of each mutant. From the extensive structural analysis, it is clear that enzyme flexibility, especially in the region of Val 217A, is primarily responsible for the exceptionally broad specificity observed in either mutant. Taken together, the observed patterns of substrate specificity can be understood to arise directly from interactions between the substrate and the residues lining the specificity pocket and indirectly from interactions between peripheral regions of the protein and the active-site region that serve to modulate active-site flexibility.

-	~~{{STRUCTURE_3lpr\| PDB=3lpr \| SCENE= }}~~	+	Structural basis for broad specificity in alpha-lytic protease mutants.,Bone R, Fujishige A, Kettner CA, Agard DA Biochemistry. 1991 Oct 29;30(43):10388-98. PMID:1931963<ref>PMID:1931963</ref>

-	~~===STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_1931963}}~~	+	==See Also==
-		+	*[[Alpha-lytic protease\|Alpha-lytic protease]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3lpr~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:001931963<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alpha-lytic endopeptidase]]		[[Category: Alpha-lytic endopeptidase]]
	[[Category: Lysobacter enzymogenes]]		[[Category: Lysobacter enzymogenes]]

OCA: Protected "3lpr" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2012 10:21:35 GMT

Protected "3lpr" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:21, 12 December 2012

OCA at 10:21, 12 December 2012

OCA — Wed, 12 Dec 2012 10:21:33 GMT

←Older revision		Revision as of 10:21, 12 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3lpr.png\|left\|200px]]		[[Image:3lpr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lpr", creates the "Structure Box" on the page.
-	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),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3lpr\| PDB=3lpr \| SCENE= }}		{{STRUCTURE_3lpr\| PDB=3lpr \| SCENE= }}

	===STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS===		===STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1931963}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1931963 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_1931963}}		{{ABSTRACT_PUBMED_1931963}}

	==About this Structure==		==About this Structure==
-	~~3LPR~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA].	+	[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~1931963~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:001931963</ref><references group="xtra"/>
	[[Category: Alpha-lytic endopeptidase]]		[[Category: Alpha-lytic endopeptidase]]
	[[Category: Lysobacter enzymogenes]]		[[Category: Lysobacter enzymogenes]]
	[[Category: Agard, D A.]]		[[Category: Agard, D A.]]
	[[Category: Bone, R.]]		[[Category: Bone, R.]]
-		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 19~~:~~49:00 2009''~~	+	[[Category: Serine proteinase]]

OCA at 17:49, 17 February 2009

OCA — Tue, 17 Feb 2009 17:49:02 GMT

←Older revision		Revision as of 17:49, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3LPR is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA].	+	3LPR is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA].

	==Reference==		==Reference==
-	~~Structural basis for broad specificity in alpha-lytic protease mutants., Bone R, Fujishige A, Kettner CA, Agard DA, Biochemistry. 1991 Oct 29;30(43):10388-98.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/1931963 1931963]~~	+	<ref group="xtra">PMID:1931963</ref><references group="xtra"/>
	[[Category: Alpha-lytic endopeptidase]]		[[Category: Alpha-lytic endopeptidase]]
	[[Category: Lysobacter enzymogenes]]		[[Category: Lysobacter enzymogenes]]
-	[[Category: Single protein]]
	[[Category: Agard, D A.]]		[[Category: Agard, D A.]]
	[[Category: Bone, R.]]		[[Category: Bone, R.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 12~~:53:~~44 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:49:00 2009''

OCA at 09:53, 3 July 2008

OCA — Thu, 03 Jul 2008 09:53:44 GMT

←Older revision		Revision as of 09:53, 3 July 2008
Line 1:		Line 1:
-	[[Image:3lpr.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3lpr.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_3lpr\| PDB=3lpr \| SCENE= }}		{{STRUCTURE_3lpr\| PDB=3lpr \| SCENE= }}

-	~~'''~~STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS~~'''~~	+	===STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS===


-	~~==Overview==~~	+	<!--
-	~~Binding pocket mutants of alpha~~-~~lytic protease (Met 192~~-~~---Ala and Met 213----Ala) have been constructed recently in an effort to create a protease specific for Met just prior to the scissile bond. Instead~~, ~~mutation resulted in proteases with extraordinarily broad specificity profiles and high activity [Bone~~, ~~R., Silen, J. L., & Agard, D. A. (1989) Nature 339, 191-195]. To understand~~ the structural basis for the unexpected specificity profiles of these mutants, high-resolution X-ray crystal structures have been determined for complexes of each mutant with a series of systematically varying peptidylboronic acids. These inhibitory analogues of high-energy reaction intermediates provide models for how substrates with different side chains interact with the enzyme during the transition state. Fifteen structures have been analyzed qualitatively and quantitatively with respect to ~~enzyme-inhibitor hydrogen-bond lengths, buried hydrophobic surface area, unfilled cavity volume, and~~ the ~~magnitude of inhibitor accommodating conformational adjustments~~ (particularly in the region of another binding pocket residue, Val 217A). Comparison of these four parameters with the Ki of each inhibitor and the kcat and Km of the analogous substrates indicates that while no single structural parameter consistently correlates with activity or inhibition, the observed data can be understood as ~~a combination of effects~~. ~~Furthermore, the relative contribution of each term differs for the three enzymes, reflecting the altered conformational energetics of each mutant~~. ~~From the extensive structural analysis~~, it is ~~clear that enzyme flexibility, especially in~~ the ~~region of Val 217A, is primarily responsible for the exceptionally broad specificity observed in either mutant~~. Taken together, the observed patterns of substrate specificity can be understood to arise directly from interactions between the substrate and the residues lining the specificity pocket and indirectly from interactions between peripheral regions of the protein and the active-~~site region that serve to modulate active~~-~~site flexibility.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_1931963}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 1931963 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_1931963}}

	==About this Structure==		==About this Structure==
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	[[Category: Agard, D A.]]		[[Category: Agard, D A.]]
	[[Category: Bone, R.]]		[[Category: Bone, R.]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:06:06 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 12:53:44 2008''

OCA at 19:06, 4 May 2008

OCA — Sun, 04 May 2008 19:06:08 GMT

←Older revision		Revision as of 19:06, 4 May 2008
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	[[Image:3lpr.gif\|left\|200px]]		[[Image:3lpr.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 3lpr \|SIZE=350\|CAPTION= <scene name='initialview01'>3lpr</scene>~~, ~~resolution 2~~.~~15Å~~	+	The line below this paragraph, containing "STRUCTURE_3lpr", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>~~, ~~<scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY= <span class='plainlinks'>[http://en~~.~~wikipedia.org/wiki/Alpha~~-~~lytic_endopeptidase Alpha~~-~~lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </span~~>	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	\|~~DOMAIN~~=	+	{{STRUCTURE_3lpr\| PDB=3lpr \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://www.ebi.ac.uk/pdbsum/3lpr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB]</span>	+
-	}}	+

	'''STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS'''		'''STRUCTURAL BASIS FOR BROAD SPECIFICITY IN ALPHA-LYTIC PROTEASE MUTANTS'''
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	[[Category: Agard, D A.]]		[[Category: Agard, D A.]]
	[[Category: Bone, R.]]		[[Category: Bone, R.]]
-	~~[[Category: hydrolase (serine proteinase)]]~~	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:06:06 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:34:26 2008''	+

←Older revision		Revision as of 07:37, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LPR FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lpr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LPR FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNO:NORLEUCINE+BORONIC+ACID'>BNO</scene>, <scene name='pdbligand=MSU:SUCCINIC+ACID+MONOMETHYL+ESTER'>MSU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-lytic_endopeptidase Alpha-lytic endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.12 3.4.21.12] </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=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB], [http://www.ebi.ac.uk/pdbsum/3lpr 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=3lpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lpr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lpr RCSB], [http://www.ebi.ac.uk/pdbsum/3lpr PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Alpha-lytic endopeptidase]]		[[Category: Alpha-lytic endopeptidase]]
	[[Category: Lysobacter enzymogenes]]		[[Category: Lysobacter enzymogenes]]
-	[[Category: Agard, D A.]]	+	[[Category: Agard, D A]]
-	[[Category: Bone, R.]]	+	[[Category: Bone, R]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Serine proteinase]]		[[Category: Serine proteinase]]