2fbp: Difference between revisions

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[[Image:2fbp.jpg|left|200px]]


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==STRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCTOSE 2,6-BISPHOSPHATE COMPLEX AT 2.8 ANGSTROMS RESOLUTION==
The line below this paragraph, containing "STRUCTURE_2fbp", creates the "Structure Box" on the page.
<StructureSection load='2fbp' size='340' side='right'caption='[[2fbp]], [[Resolution|resolution]] 2.80&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'>[[2fbp]] is a 2 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=2FBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FBP 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]] 2.8&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fbp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fbp OCA], [https://pdbe.org/2fbp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fbp RCSB], [https://www.ebi.ac.uk/pdbsum/2fbp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fbp ProSAT]</span></td></tr>
{{STRUCTURE_2fbp| PDB=2fbp |  SCENE= }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/F16P1_PIG F16P1_PIG]
== 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/fb/2fbp_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=2fbp ConSurf].
<div style="clear:both"></div>


'''STRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCTOSE 2,6-BISPHOSPHATE COMPLEX AT 2.8 ANGSTROMS RESOLUTION'''
==See Also==
 
*[[Fructose-1%2C6-bisphosphatase 3D structures|Fructose-1%2C6-bisphosphatase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The structures of the native fructose-1,6-bisphosphatase (Fru-1,6-Pase), from pig kidney cortex, and its fructose 2,6-bisphosphate (Fru-2,6-P2) complexes have been refined to 2.8 A resolution to R-factors of 0.194 and 0.188, respectively. The root-mean-square deviations from the standard geometry are 0.021 A and 0.016 A for the bond length, and 4.4 degrees and 3.8 degrees for the bond angle. Four sites for Fru-2,6-P2 binding per tetramer have been identified by difference Fourier techniques. The Fru-2,6-P2 site has the shape of an oval cave about 10 A deep, and with other dimensions about 18 A by 12 A. The two Fru-2,6-P2 binding caves of the dimer in the crystallographically asymmetric unit sit next to one another and open in opposite directions. These two binding sites mutually exchange their Arg243 side-chains, indicating the potential for communication between the two sites. The beta, D-fructose 2,6-bisphosphate has been built into the density and refined well. The oxygen atoms of the 6-phosphate group of Fru-2,6-P2 interact with Arg243 from the adjacent monomer and the residues of Lys274, Asn212, Tyr264, Tyr215 and Tyr244 in the same monomer. The sugar ring primarily contacts with the backbone atoms from Gly246 to Met248, as well as the side-chain atoms, Asp121, Glu280 and Lys274. The 2-phosphate group interacts with the side-chain atoms of Ser124 and Lys274. A negatively charged pocket near the 2-phosphate group includes Asp118, Asp121 and Glu280, as well as Glu97 and Glu98. The 2-phosphate group showed a disordered binding perhaps because of the disturbance from the negatively charged pocket. In addition, Asn125 and Lys269 are located within a 5 A radius of Fru-2,6-P2. We argue that Fru-2,6-P2 binds to the active site of the enzyme on the basis of the following observations: (1) the structure similarity between Fru-2,6-P2 and the substrate; (2) sequence conservation of the residues directly interacting with Fru-2,6-P2 or located at the negatively charged pocket; (3) a divalent metal site next to the 2-phosphate group of Fru-2,6-P2; and (4) identification of some active site residues in our structure, e.g. tyrosine and Lys274, consistent with the results of the ultraviolet spectra and the chemical modification. The structures are described in detail including interactions of interchain surfaces, and the chemically modifiable residues are discussed on the basis of the refined structures.(ABSTRACT TRUNCATED AT 400 WORDS)
[[Category: Large Structures]]
 
==About this Structure==
2FBP is a [[Single protein]] structure of 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=2FBP OCA].
 
==Reference==
Structure refinement of fructose-1,6-bisphosphatase and its fructose 2,6-bisphosphate complex at 2.8 A resolution., Ke HM, Thorpe CM, Seaton B, Lipscomb WN, Marcus F, J Mol Biol. 1990 Apr 5;212(3):513-39. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2157849 2157849]
[[Category: Fructose-bisphosphatase]]
[[Category: Single protein]]
[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
[[Category: Ke, H.]]
[[Category: Ke H]]
[[Category: Lipscomb, W N.]]
[[Category: Lipscomb WN]]
[[Category: Marcus, F.]]
[[Category: Marcus F]]
[[Category: Seaton, B A.]]
[[Category: Seaton BA]]
[[Category: Thorpe, C M.]]
[[Category: Thorpe CM]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 03:42:00 2008''

Latest revision as of 12:22, 14 February 2024

STRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCTOSE 2,6-BISPHOSPHATE COMPLEX AT 2.8 ANGSTROMS RESOLUTIONSTRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCTOSE 2,6-BISPHOSPHATE COMPLEX AT 2.8 ANGSTROMS RESOLUTION

Structural highlights

2fbp is a 2 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 2.8Å
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

2fbp, resolution 2.80Å

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