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1f65

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[[Image:1f65.gif|left|200px]]
 
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==CRYSTAL STRUCTURE OF OXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)==
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The line below this paragraph, containing "STRUCTURE_1f65", creates the "Structure Box" on the page.
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<StructureSection load='1f65' size='340' side='right'caption='[[1f65]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_1f65| PDB=1f65 | SCENE= }}
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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=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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/1f65_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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'''CRYSTAL STRUCTURE OF OXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)'''
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==See Also==
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*[[Myoglobin 3D structures|Myoglobin 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Large Structures]]
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==About this Structure==
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1F65 is a [[Single protein]] structure of sequence from [http://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].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/10049310 10049310]
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[[Category: Physeter catodon]]
[[Category: Physeter catodon]]
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[[Category: Single protein]]
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[[Category: Brunori M]]
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[[Category: Brunori, M.]]
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[[Category: Cutruzzola F]]
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[[Category: Cutruzzola, F.]]
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[[Category: Gibson QH]]
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[[Category: Gibson, Q H.]]
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[[Category: Savino C]]
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[[Category: Savino, C.]]
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[[Category: Travaglini-Allocatelli C]]
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[[Category: Travaglini-Allocatelli, C.]]
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[[Category: Vallone B]]
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[[Category: Vallone, B.]]
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[[Category: Heme]]
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[[Category: Myoglobin]]
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[[Category: Triple mutant]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:56:58 2008''
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Current revision

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

PDB ID 1f65

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