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==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='2f3b' size='340' side='right' caption='[[2f3b]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='2f3b' size='340' side='right'caption='[[2f3b]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2f3b]] 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=2F3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F3B FirstGlance]. <br>
<table><tr><td colspan='2'>[[2f3b]] 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=2F3B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F3B FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.8&#8491;</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]], [[2f3d|2f3d]], [[2f3h|2f3h]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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=2f3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3b OCA], [https://pdbe.org/2f3b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f3b RCSB], [https://www.ebi.ac.uk/pdbsum/2f3b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f3b ProSAT]</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=2f3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f3b OCA], [http://pdbe.org/2f3b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f3b RCSB], [http://www.ebi.ac.uk/pdbsum/2f3b PDBsum]</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]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/2f3b_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f3/2f3b_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>
   </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=2f3b 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--&gt;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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2f3b" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Fructose-1%2C6-bisphosphatase|Fructose-1%2C6-bisphosphatase]]
*[[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: 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 diengagement]]

Latest revision as of 12:21, 14 February 2024

Mechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphataseMechanism of displacement of a catalytically essential loop from the active site of fructose-1,6-bisphosphatase

Structural highlights

2f3b is a 1 chain structure with sequence from Sus scrofa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

F16P1_PIG

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2f3b, resolution 1.80Å

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