2f3d - Revision history

OCA at 09:21, 14 February 2024

2024-02-14T09:21:12Z

← Older revision		Revision as of 09:21, 14 February 2024
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	<StructureSection load='2f3d' size='340' side='right'caption='[[2f3d]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='2f3d' size='340' side='right'caption='[[2f3d]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F3D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F3D FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=F6P:FRUCTOSE~~-~~6-PHOSPHATE'>F6P</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</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]] 1.83Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1cnq\|1cnq]], [[1eyi\|1eyi]], [[1yxi\|1yxi]], [[1yyz\|1yyz]], [[1yzo\|1yzo]], [[1q9d\|1q9d]], [[2f3b\|2f3b]], [[2f3h\|2f3h]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=F6P:FRUCTOSE-6-PHOSPHATE'>F6P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">FBP1~~, ~~FBP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])~~<~~/td></tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11]~~ </~~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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [https://pdbe.org/2f3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [https://www.ebi.ac.uk/pdbsum/2f3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f3d 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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [https://pdbe.org/2f3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [https://www.ebi.ac.uk/pdbsum/2f3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f3d ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/F16P1_PIG F16P1_PIG]
	== 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=2f3d 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=2f3d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	AMP triggers a 15 degrees subunit-pair rotation in fructose-1,6-bisphosphatase (FBPase) from its active R-state to its inactive T-state. During this transition, a catalytically essential loop (residues 50-72) leaves its active (engaged) conformation. Structures of Ile10-->Asp FBPase and molecular dynamic simulations here reveal factors responsible for loop displacement. AMP/Mg2+ and AMP/Zn2+ complexes of Asp10 FBPase are in intermediate quaternary conformations (completing 12 degrees of subunit-pair rotation), but the complex with Zn2+ provides the first instance of an engaged loop in a near-T quaternary state. The 12 degrees subunit-pair rotation generates close contacts involving the hinges (residues 50-57) and hairpin turns (residues 58-72) of the engaged loops. Additional subunit-pair rotation toward the T-state would make such contacts unfavorable, presumably causing displacement of the loop. Targeted molecular dynamics simulations reveal no steric barriers to subunit-pair rotations up to 14 degrees , followed by the displacement of the loop from the active site. Principal component analysis reveals high-amplitude motions that exacerbate steric clashes of engaged loops in the near-T state. The results of simulations and crystal structures are in agreement: subunit-pair rotations just short of the canonical T-state, coupled with high-amplitude modes, sterically displace the dynamic loop from the active site.

	Mechanism of Displacement of a Catalytically Essential Loop from the Active Site of Mammalian Fructose-1,6-bisphosphatase.,Gao Y, Iancu CV, Mukund S, Choe JY, Honzatko RB Biochemistry. 2013 Jul 11. PMID:23844654<ref>PMID:23844654</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2f3d" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Fructose-1%2C6-bisphosphatase 3D structures\|Fructose-1%2C6-bisphosphatase 3D structures]]		*[[Fructose-1%2C6-bisphosphatase 3D structures\|Fructose-1%2C6-bisphosphatase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Fructose-bisphosphatase]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Pig~~]]		[[Category: Sus scrofa]]
	[[Category: Choe, J Y]]		[[Category: Choe J-Y]]
	[[Category: Fromm~~, H J~~]]		[[Category: Fromm HJ]]
	[[Category: Honzatko~~, R B~~]]		[[Category: Honzatko RB]]
	[[Category: Iancu~~, C V~~]]		[[Category: Iancu CV]]
	[[Category: Mukund, S]]		[[Category: Mukund S]]
	~~[[Category: 6-bisphosphatase]]~~
	~~[[Category: Allosteric regulation]]~~
	~~[[Category: Allostery]]~~
	~~[[Category: Enzyme catalysis]]~~
	~~[[Category: Fbpase]]~~
	~~[[Category: Fructose-1]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Loop displacement~~]]

OCA at 09:18, 24 February 2021

2021-02-24T09:18:37Z

@@ Line 1: / Line 1: @@
-====
+==Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase==
-<StructureSection load='2f3d' size='340' side='right'caption='[[2f3d]]' scene=''>
+<StructureSection load='2f3d' size='340' side='right'caption='[[2f3d]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2f3d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F3D FirstGlance]. <br>
-</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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [https://pdbe.org/2f3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [https://www.ebi.ac.uk/pdbsum/2f3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f3d ProSAT]</span></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=F6P:FRUCTOSE-6-PHOSPHATE'>F6P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 16: / Line 20: @@
 </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=2f3d ConSurf].
 <div style="clear:both"></div>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Z-disk]]
+[[Category: Pig]]

OCA at 07:12, 24 February 2021

2021-02-24T07:12:44Z

← Older revision		Revision as of 07:12, 24 February 2021
Line 1:		Line 1:

	==~~Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase~~==		====
	<StructureSection load='2f3d' size='340' side='right' caption='[[2f3d]]~~, [[Resolution\|resolution]] 1.83Å~~' scene=''>		<StructureSection load='2f3d' size='340' side='right'caption='[[2f3d]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[2f3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=~~2F3D~~ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=~~2F3D~~ FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=F6P:FRUCTOSE-6-PHOSPHATE'>F6P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [https://pdbe.org/2f3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [https://www.ebi.ac.uk/pdbsum/2f3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f3d ProSAT]</span></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cnq\|1cnq]], [[1eyi\|1eyi]], [[1yxi\|1yxi]], [[1yyz\|1yyz]], [[1yzo\|1yzo]], [[1q9d\|1q9d]], [[2f3b\|2f3b]], [[2f3h\|2f3h]]</td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>~~
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [~~http~~://pdbe.org/2f3d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2f3d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2f3d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 10:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/2f3d_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/2f3d_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>
Line 20:		Line 16:
	</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=2f3d 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=2f3d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	AMP triggers a 15 degrees subunit-pair rotation in fructose-1,6-bisphosphatase (FBPase) from its active R-state to its inactive T-state. During this transition, a catalytically essential loop (residues 50-72) leaves its active (engaged) conformation. Structures of Ile10-->Asp FBPase and molecular dynamic simulations here reveal factors responsible for loop displacement. AMP/Mg2+ and AMP/Zn2+ complexes of Asp10 FBPase are in intermediate quaternary conformations (completing 12 degrees of subunit-pair rotation), but the complex with Zn2+ provides the first instance of an engaged loop in a near-T quaternary state. The 12 degrees subunit-pair rotation generates close contacts involving the hinges (residues 50-57) and hairpin turns (residues 58-72) of the engaged loops. Additional subunit-pair rotation toward the T-state would make such contacts unfavorable, presumably causing displacement of the loop. Targeted molecular dynamics simulations reveal no steric barriers to subunit-pair rotations up to 14 degrees , followed by the displacement of the loop from the active site. Principal component analysis reveals high-amplitude motions that exacerbate steric clashes of engaged loops in the near-T state. The results of simulations and crystal structures are in agreement: subunit-pair rotations just short of the canonical T-state, coupled with high-amplitude modes, sterically displace the dynamic loop from the active site.

	Mechanism of Displacement of a Catalytically Essential Loop from the Active Site of Mammalian Fructose-1,6-bisphosphatase.,Gao Y, Iancu CV, Mukund S, Choe JY, Honzatko RB Biochemistry. 2013 Jul 11. PMID:23844654<ref>PMID:23844654</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2f3d" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Fructose-bisphosphatase]]~~		[[Category: Large Structures]]
	~~[[Category: Pig]]~~		[[Category: Z-disk]]
	~~[[Category: Choe, J Y]]~~
	~~[[Category: Fromm, H J~~]]
	[[Category: ~~Honzatko, R B]]~~
	~~[[Category: Iancu, C V]]~~
	~~[[Category: Mukund, S]]~~
	~~[[Category: 6~~-~~bisphosphatase]]~~
	~~[[Category: Allosteric regulation]]~~
	~~[[Category: Allostery]]~~
	~~[[Category: Enzyme catalysis]]~~
	~~[[Category: Fbpase]]~~
	~~[[Category: Fructose-1]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Loop displacement~~]]

OCA at 07:33, 18 October 2017

2017-10-18T07:33:05Z

← Older revision		Revision as of 07:33, 18 October 2017
Line 1:		Line 1:

	==Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase==		==Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase==
	<StructureSection load='2f3d' size='340' side='right' caption='[[2f3d]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='2f3d' size='340' side='right' caption='[[2f3d]], [[Resolution\|resolution]] 1.83Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [http://pdbe.org/2f3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [http://www.ebi.ac.uk/pdbsum/2f3d 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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [http://pdbe.org/2f3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [http://www.ebi.ac.uk/pdbsum/2f3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f3d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2f3d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2f3d" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Fructose-1%2C6-bisphosphatase\|Fructose-1%2C6-bisphosphatase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:44, 7 February 2016

2016-02-07T05:44:52Z

← Older revision		Revision as of 05:44, 7 February 2016
Line 17:		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=2f3d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:25, 9 September 2015

2015-09-09T22:25:24Z

← Older revision		Revision as of 22:25, 9 September 2015
Line 7:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [http://www.ebi.ac.uk/pdbsum/2f3d 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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [http://pdbe.org/2f3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [http://www.ebi.ac.uk/pdbsum/2f3d PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		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 2f3d" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 18:34, 15 January 2015

2015-01-15T18:34:56Z

← Older revision		Revision as of 18:34, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F3D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F3D FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=F6P:FRUCTOSE-6-PHOSPHATE'>F6P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=F6P:FRUCTOSE-6-PHOSPHATE'>F6P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cnq\|1cnq]], [[1eyi\|1eyi]], [[1yxi\|1yxi]], [[1yyz\|1yyz]], [[1yzo\|1yzo]], [[1q9d\|1q9d]], [[2f3b\|2f3b]], [[2f3h\|2f3h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cnq\|1cnq]], [[1eyi\|1eyi]], [[1yxi\|1yxi]], [[1yyz\|1yyz]], [[1yzo\|1yzo]], [[1q9d\|1q9d]], [[2f3b\|2f3b]], [[2f3h\|2f3h]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [http://www.ebi.ac.uk/pdbsum/2f3d 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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [http://www.ebi.ac.uk/pdbsum/2f3d PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Fructose-bisphosphatase]]		[[Category: Fructose-bisphosphatase]]
	[[Category: Pig]]		[[Category: Pig]]
	[[Category: Choe, J Y.]]		[[Category: Choe, J Y]]
	[[Category: Fromm, H J.]]		[[Category: Fromm, H J]]
	[[Category: Honzatko, R B.]]		[[Category: Honzatko, R B]]
	[[Category: Iancu, C V.]]		[[Category: Iancu, C V]]
	[[Category: Mukund, S.]]		[[Category: Mukund, S]]
	[[Category: 6-bisphosphatase]]		[[Category: 6-bisphosphatase]]
	[[Category: Allosteric regulation]]		[[Category: Allosteric regulation]]

OCA at 05:37, 3 October 2014

2014-10-03T05:37:26Z

← Older revision		Revision as of 05:37, 3 October 2014
Line 1:		Line 1:
	~~{{STRUCTURE_2f3d\| PDB=2f3d \| SCENE= }}~~		==Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase==
	===Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase===		<StructureSection load='2f3d' size='340' side='right' caption='[[2f3d]], [[Resolution\|resolution]] 1.83Å' scene=''>
	~~{{ABSTRACT_PUBMED_23844654}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2f3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F3D FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=F6P:FRUCTOSE-6-PHOSPHATE'>F6P</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1cnq\|1cnq]], [[1eyi\|1eyi]], [[1yxi\|1yxi]], [[1yyz\|1yyz]], [[1yzo\|1yzo]], [[1q9d\|1q9d]], [[2f3b\|2f3b]], [[2f3h\|2f3h]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FBP1, FBP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphatase Fructose-bisphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.11 3.1.3.11] </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=2f3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f3d RCSB], [http://www.ebi.ac.uk/pdbsum/2f3d 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/f3/2f3d_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 ==
			AMP triggers a 15 degrees subunit-pair rotation in fructose-1,6-bisphosphatase (FBPase) from its active R-state to its inactive T-state. During this transition, a catalytically essential loop (residues 50-72) leaves its active (engaged) conformation. Structures of Ile10-->Asp FBPase and molecular dynamic simulations here reveal factors responsible for loop displacement. AMP/Mg2+ and AMP/Zn2+ complexes of Asp10 FBPase are in intermediate quaternary conformations (completing 12 degrees of subunit-pair rotation), but the complex with Zn2+ provides the first instance of an engaged loop in a near-T quaternary state. The 12 degrees subunit-pair rotation generates close contacts involving the hinges (residues 50-57) and hairpin turns (residues 58-72) of the engaged loops. Additional subunit-pair rotation toward the T-state would make such contacts unfavorable, presumably causing displacement of the loop. Targeted molecular dynamics simulations reveal no steric barriers to subunit-pair rotations up to 14 degrees , followed by the displacement of the loop from the active site. Principal component analysis reveals high-amplitude motions that exacerbate steric clashes of engaged loops in the near-T state. The results of simulations and crystal structures are in agreement: subunit-pair rotations just short of the canonical T-state, coupled with high-amplitude modes, sterically displace the dynamic loop from the active site.

	~~==About this Structure==~~		Mechanism of Displacement of a Catalytically Essential Loop from the Active Site of Mammalian Fructose-1,6-bisphosphatase.,Gao Y, Iancu CV, Mukund S, Choe JY, Honzatko RB Biochemistry. 2013 Jul 11. PMID:23844654<ref>PMID:23844654</ref>
	~~[[2f3d]] is~~ a 1 ~~chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pig Pig]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.~~il/oca-bin~~/~~ocashort?id=2F3D OCA].~~
			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	==See Also==		==See Also==
	*[[Fructose-1%2C6-bisphosphatase\|Fructose-1%2C6-bisphosphatase]]		*[[Fructose-1%2C6-bisphosphatase\|Fructose-1%2C6-bisphosphatase]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:023844654</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Fructose-bisphosphatase]]		[[Category: Fructose-bisphosphatase]]
	[[Category: Pig]]		[[Category: Pig]]

OCA at 09:14, 5 February 2014

2014-02-05T09:14:59Z

← Older revision		Revision as of 09:14, 5 February 2014
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
	[[2f3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sus_scrofa Sus scrofa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA].		[[2f3d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F3D OCA].

	==See Also==		==See Also==
Line 12:		Line 12:
	<ref group="xtra">PMID:023844654</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023844654</ref><references group="xtra"/><references/>
	[[Category: Fructose-bisphosphatase]]		[[Category: Fructose-bisphosphatase]]
	[[Category: ~~Sus scrofa~~]]		[[Category: Pig]]
	[[Category: Choe, J Y.]]		[[Category: Choe, J Y.]]
	[[Category: Fromm, H J.]]		[[Category: Fromm, H J.]]

OCA at 11:39, 24 July 2013

2013-07-24T11:39:34Z

← Older revision		Revision as of 11:39, 24 July 2013
Line 1:		Line 1:
	~~[[Image:2f3d.png\|left\|200px]]~~

	{{STRUCTURE_2f3d\| PDB=2f3d \| SCENE= }}		{{STRUCTURE_2f3d\| PDB=2f3d \| SCENE= }}

	===Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase===		===Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase===
			{{ABSTRACT_PUBMED_23844654}}

	==About this Structure==		==About this Structure==
Line 11:		Line 8:
	==See Also==		==See Also==
	*[[Fructose-1%2C6-bisphosphatase\|Fructose-1%2C6-bisphosphatase]]		*[[Fructose-1%2C6-bisphosphatase\|Fructose-1%2C6-bisphosphatase]]

			==Reference==
			<ref group="xtra">PMID:023844654</ref><references group="xtra"/><references/>
	[[Category: Fructose-bisphosphatase]]		[[Category: Fructose-bisphosphatase]]
	[[Category: Sus scrofa]]		[[Category: Sus scrofa]]