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| | ==Quadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human liver fructose-1,6-bisphosphatase== | | ==Quadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human liver fructose-1,6-bisphosphatase== |
| - | <StructureSection load='5ldz' size='340' side='right' caption='[[5ldz]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='5ldz' size='340' side='right'caption='[[5ldz]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ldz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ldz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LDZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</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=9606 HUMAN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5ldz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldz OCA], [https://pdbe.org/5ldz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ldz RCSB], [https://www.ebi.ac.uk/pdbsum/5ldz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldz ProSAT]</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=5ldz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldz OCA], [http://pdbe.org/5ldz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldz RCSB], [http://www.ebi.ac.uk/pdbsum/5ldz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Disease == | | == Disease == |
| - | [[http://www.uniprot.org/uniprot/F16P1_HUMAN F16P1_HUMAN]] Defects in FBP1 are the cause of fructose-1,6-bisphosphatase deficiency (FBPD) [MIM:[http://omim.org/entry/229700 229700]]. FBPD is inherited as an autosomal recessive disorder mainly in the liver and causes life-threatening episodes of hypoglycemia and metabolic acidosis (lactacidemia) in newborn infants or young children.<ref>PMID:9382095</ref> <ref>PMID:12126934</ref> | + | [https://www.uniprot.org/uniprot/F16P1_HUMAN F16P1_HUMAN] Defects in FBP1 are the cause of fructose-1,6-bisphosphatase deficiency (FBPD) [MIM:[https://omim.org/entry/229700 229700]. FBPD is inherited as an autosomal recessive disorder mainly in the liver and causes life-threatening episodes of hypoglycemia and metabolic acidosis (lactacidemia) in newborn infants or young children.<ref>PMID:9382095</ref> <ref>PMID:12126934</ref> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/F16P1_HUMAN F16P1_HUMAN] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==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 == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Fructose-bisphosphatase]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Human]] | + | [[Category: Large Structures]] |
| - | [[Category: Joseph, C]] | + | [[Category: Joseph C]] |
| - | [[Category: Rudolph, M G]] | + | [[Category: Rudolph MG]] |
| - | [[Category: Ruf, A]] | + | [[Category: Ruf A]] |
| - | [[Category: Schott, B]] | + | [[Category: Schott B]] |
| - | [[Category: Tetaz, T]] | + | [[Category: Tetaz T]] |
| - | [[Category: Allosteric enzyme]]
| + | |
| - | [[Category: Carbohydrate]]
| + | |
| - | [[Category: Gluconeogenesis]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metabolism]]
| + | |
| - | [[Category: Phosphoric monoester]]
| + | |
| Structural highlights
Disease
F16P1_HUMAN Defects in FBP1 are the cause of fructose-1,6-bisphosphatase deficiency (FBPD) [MIM:229700. FBPD is inherited as an autosomal recessive disorder mainly in the liver and causes life-threatening episodes of hypoglycemia and metabolic acidosis (lactacidemia) in newborn infants or young children.[1] [2]
Function
F16P1_HUMAN
Publication Abstract from PubMed
Fructose-1,6-bisphosphatase (FBPase) is a key regulator of gluconeogenesis and a potential drug target for type 2 diabetes. FBPase is a homotetramer of 222 symmetry with a major and a minor dimer interface. The dimers connected via the minor interface can rotate with respect to each other, leading to the inactive T-state and active R-state conformations of FBPase. Here, the first crystal structure of human liver FBPase in the R-state conformation is presented, determined at a resolution of 2.2 A in a tetragonal setting that exhibits an unusual arrangement of noncrystallographic symmetry (NCS) elements. Self-Patterson function analysis and various intensity statistics revealed the presence of pseudo-translation and the absence of twinning. The space group is P41212, but structure determination was also possible in space groups P43212, P4122 and P4322. All solutions have the same arrangement of three C2-symmetric dimers spaced by 1/3 along an NCS axis parallel to the c axis located at (1/4, 1/4, z), which is therefore invisible in a self-rotation function analysis. The solutions in the four space groups are related to one another and emulate a body-centred lattice. If all NCS elements were crystallographic, the space group would be I4122 with a c axis three times shorter and a single FBPase subunit in the asymmetric unit. I4122 is a minimal, non-isomorphic supergroup of the four primitive tetragonal space groups, explaining the space-group ambiguity for this crystal.
Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase.,Ruf A, Tetaz T, Schott B, Joseph C, Rudolph MG Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1212-1224. doi:, 10.1107/S2059798316016715. Epub 2016 Oct 28. PMID:27841754[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kikawa Y, Inuzuka M, Jin BY, Kaji S, Koga J, Yamamoto Y, Fujisawa K, Hata I, Nakai A, Shigematsu Y, Mizunuma H, Taketo A, Mayumi M, Sudo M. Identification of genetic mutations in Japanese patients with fructose-1,6-bisphosphatase deficiency. Am J Hum Genet. 1997 Oct;61(4):852-61. PMID:9382095
- ↑ Matsuura T, Chinen Y, Arashiro R, Katsuren K, Tamura T, Hyakuna N, Ohta T. Two newly identified genomic mutations in a Japanese female patient with fructose-1,6-bisphosphatase (FBPase) deficiency. Mol Genet Metab. 2002 Jul;76(3):207-10. PMID:12126934
- ↑ Ruf A, Tetaz T, Schott B, Joseph C, Rudolph MG. Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase. Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1212-1224. doi:, 10.1107/S2059798316016715. Epub 2016 Oct 28. PMID:27841754 doi:http://dx.doi.org/10.1107/S2059798316016715
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