3h57: Difference between revisions
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==Myoglobin Cavity Mutant H64LV68N Deoxy form== | |||
<StructureSection load='3h57' size='340' side='right'caption='[[3h57]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3h57]] 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=3H57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H57 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]] 1.7Å</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></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=3h57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h57 OCA], [https://pdbe.org/3h57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h57 RCSB], [https://www.ebi.ac.uk/pdbsum/3h57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h57 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/h5/3h57_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=3h57 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Internal water molecules are important to protein structure and function, but positional disorder and low occupancies can obscure their detection by X-ray crystallography. Here, we show that water can be detected within the distal cavities of myoglobin mutants by subtle changes in the absorbance spectrum of pentacoordinate heme, even when the presence of solvent is not readily observed in the corresponding crystal structures. A well-defined, noncoordinated water molecule hydrogen bonded to the distal histidine (His64) is seen within the distal heme pocket in the crystal structure of wild type (wt) deoxymyoglobin. Displacement of this water decreases the rate of ligand entry into wt Mb, and we have shown previously that the entry of this water is readily detected optically after laser photolysis of MbCO complexes. However, for L29F and V68L Mb no discrete positions for solvent molecules are seen in the electron density maps of the crystal structures even though His64 is still present and slow rates of ligand binding indicative of internal water are observed. In contrast, time-resolved perturbations of the visible absorption bands of L29F and V68L deoxyMb generated after laser photolysis detect the entry and significant occupancy of water within the distal pockets of these variants. Thus, the spectral perturbation of pentacoordinate heme offers a potentially robust system for measuring nonspecific hydration of the active sites of heme proteins. | |||
Optical detection of disordered water within a protein cavity.,Goldbeck RA, Pillsbury ML, Jensen RA, Mendoza JL, Nguyen RL, Olson JS, Soman J, Kliger DS, Esquerra RM J Am Chem Soc. 2009 Sep 2;131(34):12265-72. PMID:19655795<ref>PMID:19655795</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3h57" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Myoglobin|Myoglobin]] | *[[Myoglobin 3D structures|Myoglobin 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Physeter catodon]] | [[Category: Physeter catodon]] | ||
[[Category: Olson | [[Category: Olson JS]] | ||
[[Category: Soman | [[Category: Soman J]] | ||
Latest revision as of 10:16, 6 September 2023
Myoglobin Cavity Mutant H64LV68N Deoxy formMyoglobin Cavity Mutant H64LV68N Deoxy form
Structural highlights
FunctionMYG_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. Publication Abstract from PubMedInternal water molecules are important to protein structure and function, but positional disorder and low occupancies can obscure their detection by X-ray crystallography. Here, we show that water can be detected within the distal cavities of myoglobin mutants by subtle changes in the absorbance spectrum of pentacoordinate heme, even when the presence of solvent is not readily observed in the corresponding crystal structures. A well-defined, noncoordinated water molecule hydrogen bonded to the distal histidine (His64) is seen within the distal heme pocket in the crystal structure of wild type (wt) deoxymyoglobin. Displacement of this water decreases the rate of ligand entry into wt Mb, and we have shown previously that the entry of this water is readily detected optically after laser photolysis of MbCO complexes. However, for L29F and V68L Mb no discrete positions for solvent molecules are seen in the electron density maps of the crystal structures even though His64 is still present and slow rates of ligand binding indicative of internal water are observed. In contrast, time-resolved perturbations of the visible absorption bands of L29F and V68L deoxyMb generated after laser photolysis detect the entry and significant occupancy of water within the distal pockets of these variants. Thus, the spectral perturbation of pentacoordinate heme offers a potentially robust system for measuring nonspecific hydration of the active sites of heme proteins. Optical detection of disordered water within a protein cavity.,Goldbeck RA, Pillsbury ML, Jensen RA, Mendoza JL, Nguyen RL, Olson JS, Soman J, Kliger DS, Esquerra RM J Am Chem Soc. 2009 Sep 2;131(34):12265-72. PMID:19655795[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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