1f65: Difference between revisions

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New page: left|200px<br /><applet load="1f65" size="450" color="white" frame="true" align="right" spinBox="true" caption="1f65, resolution 1.7Å" /> '''CRYSTAL STRUCTURE OF ...
 
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[[Image:1f65.gif|left|200px]]<br /><applet load="1f65" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1f65, resolution 1.7&Aring;" />
'''CRYSTAL STRUCTURE OF OXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)'''<br />


==Overview==
==CRYSTAL STRUCTURE OF OXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)==
A triple mutant of sperm whale myoglobin (Mb) [Leu(B10) --&gt; Tyr, His(E7), --&gt; Gln, and Thr(E10) --&gt; Arg, called Mb-YQR], investigated by, stopped-flow, laser photolysis, crystallography, and molecular dynamics, (MD) simulations, proved to be quite unusual. Rebinding of, photodissociated NO, O2, and CO from within the protein (in a "geminate", mode) allows us to reach general conclusions about dynamics and cavities, in proteins. The 3D structure of oxy Mb-YQR shows that bound O2 makes two, H-bonds with Tyr(B10)29 and Gln(E7)64; on deoxygenation, these two, residues move toward the space occupied by O2. The bimolecular rate, constant for NO binding is the same as for wild-type, but those for CO and, O2 binding are reduced 10-fold. While there is no geminate recombination, with O2 and CO, geminate rebinding of NO displays an unusually large and, very slow component, which is pretty much abolished in the presence of, xenon. These results and MD simulations suggest that the ligand migrates, in the protein matrix to a major "secondary site," located beneath, Tyr(B10)29 and accessible via the motion of Ile(G8)107; this site is, different from the "primary site" identified by others who investigated, the photolyzed state of wild-type Mb by crystallography. Our hypothesis, may rationalize the O2 binding properties of Mb-YQR, and more generally to, propose a mechanism of control of ligand binding and dissociation in, hemeproteins based on the dynamics of side chains that may (or may not), allow access to and direct temporary sequestration of the dissociated, ligand in a docking site within the protein. This interpretation suggests, that very fast (picosecond) fluctuations of amino acid side chains may, play a crucial role in controlling O2 delivery to tissue at a rate, compatible with physiology.
<StructureSection load='1f65' size='340' side='right'caption='[[1f65]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1f65]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F65 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F65 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]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1f65 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f65 OCA], [https://pdbe.org/1f65 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f65 RCSB], [https://www.ebi.ac.uk/pdbsum/1f65 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f65 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
== 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/f6/1f65_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=1f65 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1F65 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon] with SO4, HEM and OXY as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1F65 OCA].
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10)., Brunori M, Cutruzzola F, Savino C, Travaglini-Allocatelli C, Vallone B, Gibson QH, Biophys J. 1999 Mar;76(3):1259-69. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10049310 10049310]
[[Category: Large Structures]]
[[Category: Physeter catodon]]
[[Category: Physeter catodon]]
[[Category: Single protein]]
[[Category: Brunori M]]
[[Category: Brunori, M.]]
[[Category: Cutruzzola F]]
[[Category: Cutruzzola, F.]]
[[Category: Gibson QH]]
[[Category: Gibson, Q.H.]]
[[Category: Savino C]]
[[Category: Savino, C.]]
[[Category: Travaglini-Allocatelli C]]
[[Category: Travaglini-Allocatelli, C.]]
[[Category: Vallone B]]
[[Category: Vallone, B.]]
[[Category: HEM]]
[[Category: OXY]]
[[Category: SO4]]
[[Category: heme]]
[[Category: myoglobin]]
[[Category: triple mutant]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:39:00 2007''

Latest revision as of 10:11, 7 February 2024

CRYSTAL STRUCTURE OF OXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)CRYSTAL STRUCTURE OF OXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)

Structural highlights

1f65 is a 1 chain structure with sequence from Physeter catodon. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MYG_PHYMC Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.

Evolutionary Conservation

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

See Also

1f65, resolution 1.70Å

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