2fbp: Difference between revisions

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New page: left|200px<br /><applet load="2fbp" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fbp, resolution 2.8Å" /> '''STRUCTURE REFINEMENT ...
 
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[[Image:2fbp.jpg|left|200px]]<br /><applet load="2fbp" size="450" color="white" frame="true" align="right" spinBox="true"
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'''STRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCTOSE 2,6-BISPHOSPHATE COMPLEX AT 2.8 ANGSTROMS RESOLUTION'''<br />


==Overview==
==STRUCTURE REFINEMENT OF FRUCTOSE-1,6-BISPHOSPHATASE AND ITS FRUCTOSE 2,6-BISPHOSPHATE COMPLEX AT 2.8 ANGSTROMS RESOLUTION==
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)
<StructureSection load='2fbp' size='340' side='right'caption='[[2fbp]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
</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>


==About this Structure==
==See Also==
2FBP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. 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=2FBP OCA].
*[[Fructose-1%2C6-bisphosphatase 3D structures|Fructose-1%2C6-bisphosphatase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=2157849 2157849]
[[Category: Large Structures]]
[[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]]
[[Category: hydrolase (phosphoric monoester)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:28:16 2007''

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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