1umg: Difference between revisions

Latest revision as of 23:56, 27 December 2023

Crystal structure of fructose-1,6-bisphosphatase

Structural highlights

1umg is a 1 chain structure with sequence from Sulfurisphaera tokodaii str. 7. 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:	2FP, MG, MPD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FBPAP_SULTO Catalyzes two subsequent steps in gluconeogenesis: the aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to fructose-1,6-bisphosphate (FBP), and the dephosphorylation of FBP to fructose-6-phosphate (F6P).^[1] ^[2] ^[3]

Evolutionary Conservation

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

Publication Abstract from PubMed

As the first structure of the novel class of fructose-1,6-bisphosphatase (FBPase) present in thermophilic archaea, we solved the crystal structure of the ST0318 gene product (St-Fbp) of Sulfolobus tokodaii strain 7. The St-Fbp structure comprises a homooctamer of the 422 point-group. The protein folds as a four-layer alpha-beta-beta-alpha sandwich with a novel topology, which is completely different from the sugar phosphatase fold. The structure contains an unhydrolyzed FBP molecule in the open-keto form, as well as four hexacoordinated magnesium ions around the 1-phosphoryl group of FBP. The arrangement of the catalytic side chains and metal ligands is consistent with the three-metal ion assisted catalysis proposed for conventional FBPases. The structure provides an insight into the structural basis of the strict substrate specificity of St-Fbp.

The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea.,Nishimasu H, Fushinobu S, Shoun H, Wakagi T Structure. 2004 Jun;12(6):949-59. PMID:15274916^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nishimasu H, Fushinobu S, Shoun H, Wakagi T. The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea. Structure. 2004 Jun;12(6):949-59. PMID:15274916 doi:10.1016/j.str.2004.03.026
↑ Say RF, Fuchs G. Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature. 2010 Apr 15;464(7291):1077-81. PMID:20348906 doi:10.1038/nature08884
↑ Fushinobu S, Nishimasu H, Hattori D, Song HJ, Wakagi T. Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase. Nature. 2011 Oct 9;478(7370):538-41. doi: 10.1038/nature10457. PMID:21983966 doi:10.1038/nature10457
↑ Nishimasu H, Fushinobu S, Shoun H, Wakagi T. The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea. Structure. 2004 Jun;12(6):949-59. PMID:15274916 doi:10.1016/j.str.2004.03.026

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Nishimasu H, Fushinobu S, Shoun H, Wakagi T. The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea. Structure. 2004 Jun;12(6):949-59. PMID:15274916 doi:10.1016/j.str.2004.03.026

[2] Say RF, Fuchs G. Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature. 2010 Apr 15;464(7291):1077-81. PMID:20348906 doi:10.1038/nature08884

[3] Fushinobu S, Nishimasu H, Hattori D, Song HJ, Wakagi T. Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase. Nature. 2011 Oct 9;478(7370):538-41. doi: 10.1038/nature10457. PMID:21983966 doi:10.1038/nature10457

[4] Nishimasu H, Fushinobu S, Shoun H, Wakagi T. The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea. Structure. 2004 Jun;12(6):949-59. PMID:15274916 doi:10.1016/j.str.2004.03.026

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-[[Image:1umg.gif|left|200px]]<br /><applet load="1umg" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1umg, resolution 1.80&Aring;" />
-'''Crystal strucure of fructose-1,6-bisphosphatase'''<br />
-==Overview==
+==Crystal structure of fructose-1,6-bisphosphatase==
-As the first structure of the novel class of fructose-1,6-bisphosphatase, (FBPase) present in thermophilic archaea, we solved the crystal structure, of the ST0318 gene product (St-Fbp) of Sulfolobus tokodaii strain 7. The, St-Fbp structure comprises a homooctamer of the 422 point-group. The, protein folds as a four-layer alpha-beta-beta-alpha sandwich with a novel, topology, which is completely different from the sugar phosphatase fold., The structure contains an unhydrolyzed FBP molecule in the open-keto form, as well as four hexacoordinated magnesium ions around the 1-phosphoryl, group of FBP. The arrangement of the catalytic side chains and metal, ligands is consistent with the three-metal ion assisted catalysis proposed, for conventional FBPases. The structure provides an insight into the, structural basis of the strict substrate specificity of St-Fbp.
+<StructureSection load='1umg' size='340' side='right'caption='[[1umg]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1umg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UMG FirstGlance]. <br>
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2FP:1,6-FRUCTOSE+DIPHOSPHATE+(LINEAR+FORM)'>2FP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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=1umg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1umg OCA], [https://pdbe.org/1umg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1umg RCSB], [https://www.ebi.ac.uk/pdbsum/1umg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1umg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FBPAP_SULTO FBPAP_SULTO] Catalyzes two subsequent steps in gluconeogenesis: the aldol condensation of dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GA3P) to fructose-1,6-bisphosphate (FBP), and the dephosphorylation of FBP to fructose-6-phosphate (F6P).<ref>PMID:15274916</ref> <ref>PMID:20348906</ref> <ref>PMID:21983966</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/um/1umg_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=1umg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+As the first structure of the novel class of fructose-1,6-bisphosphatase (FBPase) present in thermophilic archaea, we solved the crystal structure of the ST0318 gene product (St-Fbp) of Sulfolobus tokodaii strain 7. The St-Fbp structure comprises a homooctamer of the 422 point-group. The protein folds as a four-layer alpha-beta-beta-alpha sandwich with a novel topology, which is completely different from the sugar phosphatase fold. The structure contains an unhydrolyzed FBP molecule in the open-keto form, as well as four hexacoordinated magnesium ions around the 1-phosphoryl group of FBP. The arrangement of the catalytic side chains and metal ligands is consistent with the three-metal ion assisted catalysis proposed for conventional FBPases. The structure provides an insight into the structural basis of the strict substrate specificity of St-Fbp.
-==About this Structure==
+The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea.,Nishimasu H, Fushinobu S, Shoun H, Wakagi T Structure. 2004 Jun;12(6):949-59. PMID:15274916<ref>PMID:15274916</ref>
-UMG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_tokodaii Sulfolobus tokodaii] with MG, 2FP and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UMG OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The first crystal structure of the novel class of fructose-1,6-bisphosphatase present in thermophilic archaea., Nishimasu H, Fushinobu S, Shoun H, Wakagi T, Structure. 2004 Jun;12(6):949-59. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15274916 15274916]
+</div>
-[[Category: Fructose-bisphosphatase]]
+<div class="pdbe-citations 1umg" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Sulfolobus tokodaii]]
-[[Category: Fushinobu, S.]]
-[[Category: Nishimasu, H.]]
-[[Category: Shoun, H.]]
-[[Category: Wakagi, T.]]
-[[Category: 2FP]]
-[[Category: MG]]
-[[Category: MPD]]
-[[Category: 6-bisphosphatase]]
-[[Category: alpha-beta-beta-alpha four layer sandwich]]
-[[Category: fructose-1]]
-[[Category: hyperthermophilic archaea]]
-[[Category: magnesium ion]]
-[[Category: octamer]]
-[[Category: phosphatase]]
-[[Category: three metal-assisted mechanism]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:12:56 2007''
+==See Also==
+*[[Fructose-1%2C6-bisphosphatase 3D structures|Fructose-1%2C6-bisphosphatase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Sulfurisphaera tokodaii str. 7]]
+[[Category: Fushinobu S]]
+[[Category: Nishimasu H]]
+[[Category: Shoun H]]
+[[Category: Wakagi T]]

1umg: Difference between revisions

Latest revision as of 23:56, 27 December 2023

Crystal structure of fructose-1,6-bisphosphatase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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