3big: Difference between revisions

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-{{Seed}}
-[[Image:3big.png|left|200px]]
-<!--
+==Crystal structure of the fructose-1,6-bisphosphatase GlpX from E.coli in complex with inorganic phosphate==
-The line below this paragraph, containing "STRUCTURE_3big", creates the "Structure Box" on the page.
+<StructureSection load='3big' size='340' side='right'caption='[[3big]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3big]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BIG FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-{{STRUCTURE_3big|  PDB=3big  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3big FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3big OCA], [https://pdbe.org/3big PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3big RCSB], [https://www.ebi.ac.uk/pdbsum/3big PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3big ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLPX_ECOLI GLPX_ECOLI] Catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate. Is likely to be involved in gluconeogenesis during growth on glycerol. Also displays a low activity toward glucose 1,6-bisphosphate, and no activity against ribulose 1,5-bisphosphate, fructose 2,6-bisphosphate, or fructose 1-phosphate.<ref>PMID:10986273</ref> <ref>PMID:19073594</ref>
+== 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/bi/3big_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/main_output.php?pdb_ID=3big ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Gluconeogenesis is an important metabolic pathway, which produces glucose from noncarbohydrate precursors such as organic acids, fatty acids, amino acids, or glycerol. Fructose-1,6-bisphosphatase, a key enzyme of gluconeogenesis, is found in all organisms, and five different classes of these enzymes have been identified. Here we demonstrate that Escherichia coli has two class II fructose-1,6-bisphosphatases, GlpX and YggF, which show different catalytic properties. We present the first crystal structure of a class II fructose-1,6-bisphosphatase (GlpX) determined in a free state and in the complex with a substrate (fructose 1,6-bisphosphate) or inhibitor (phosphate). The crystal structure of the ligand-free GlpX revealed a compact, globular shape with two alpha/beta-sandwich domains. The core fold of GlpX is structurally similar to that of Li+-sensitive phosphatases implying that they have a common evolutionary origin and catalytic mechanism. The structure of the GlpX complex with fructose 1,6-bisphosphate revealed that the active site is located between two domains and accommodates several conserved residues coordinating two metal ions and the substrate. The third metal ion is bound to phosphate 6 of the substrate. Inorganic phosphate strongly inhibited activity of both GlpX and YggF, and the crystal structure of the GlpX complex with phosphate demonstrated that the inhibitor molecule binds to the active site. Alanine replacement mutagenesis of GlpX identified 12 conserved residues important for activity and suggested that Thr(90) is the primary catalytic residue. Our data provide insight into the molecular mechanisms of the substrate specificity and catalysis of GlpX and other class II fructose-1,6-bisphosphatases.
-===Crystal structure of the fructose-1,6-bisphosphatase GlpX from E.coli in complex with inorganic phosphate===
+Structural and biochemical characterization of the type II fructose-1,6-bisphosphatase GlpX from Escherichia coli.,Brown G, Singer A, Lunin VV, Proudfoot M, Skarina T, Flick R, Kochinyan S, Sanishvili R, Joachimiak A, Edwards AM, Savchenko A, Yakunin AF J Biol Chem. 2009 Feb 6;284(6):3784-92. Epub 2008 Dec 10. PMID:19073594<ref>PMID:19073594</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3big" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19073594}}, adds the Publication Abstract to the page
+*[[Fructose-1%2C6-bisphosphatase 3D structures|Fructose-1%2C6-bisphosphatase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19073594 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19073594}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-BIG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k12 Escherichia coli k12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BIG OCA].
+[[Category: Large Structures]]
+[[Category: Brown G]]
-==Reference==
+[[Category: Edwards AM]]
-Structural and Biochemical Characterization of the Type II Fructose-1,6-bisphosphatase GlpX from Escherichia coli., Brown G, Singer A, Lunin VV, Proudfoot M, Skarina T, Flick R, Kochinyan S, Sanishvili R, Joachimiak A, Edwards AM, Savchenko A, Yakunin AF, J Biol Chem. 2009 Feb 6;284(6):3784-92. Epub 2008 Dec 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19073594 19073594]
+[[Category: Lunin VV]]
-[[Category: Escherichia coli k12]]
+[[Category: Savchenko A]]
-[[Category: Fructose-bisphosphatase]]
+[[Category: Skarina T]]
-[[Category: Single protein]]
+[[Category: Yakunin AF]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-[[Category: 6-bisphosphatase]]
-[[Category: Carbohydrate metabolism]]
-[[Category: Cytoplasm]]
-[[Category: Glpx]]
-[[Category: Hydrolase]]
-[[Category: Manganese]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 11 20:03:37 2009''