1vxc: Difference between revisions

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-[[Image:1vxc.gif|left|200px]]
-<!--
+==NATIVE SPERM WHALE MYOGLOBIN==
-The line below this paragraph, containing "STRUCTURE_1vxc", creates the "Structure Box" on the page.
+<StructureSection load='1vxc' size='340' side='right'caption='[[1vxc]], [[Resolution|resolution]] 1.70&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'>[[1vxc]] 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=1VXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VXC 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1vxc|  PDB=1vxc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vxc OCA], [https://pdbe.org/1vxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vxc RCSB], [https://www.ebi.ac.uk/pdbsum/1vxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vxc 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/vx/1vxc_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=1vxc ConSurf].
+<div style="clear:both"></div>
-'''NATIVE SPERM WHALE MYOGLOBIN'''
+==See Also==
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-The distal histidine residue, His64(E7), and the proximal histidine residue, His93(F8), in myoglobin (Mb) are important for the function of the protein. For example, the increase in the association rate constant for CO binding at low pH has been suggested to be caused by the protonation of these histidine residues. In order to investigate the influence of protonation on the structure of myoglobin, we determined the crystal structures of sperm whale myoglobin to 2.0 A or better in different states of ligation (MbCO, deoxyMb and metMb) at pH values of 4, 5 and 6. The most dramatic change found at low pH is that His64 swings out of the distal pocket in the MbCO structure at pH 4, opening a direct channel from the solvent to the iron atom. This rotation seems to be facilitated by conformational changes in the CD corner. The benzyl side-chain of Phe46(CD4), which has been suggested to be a critical residue in controlling the rotation of His64, moves away from His64 at pH 4 in the deoxyMb structure, allowing more free rotation of His64. Arg45(CD3) is also important for the dynamics of myoglobin, since it influences the pK(a) of His64 and forms a hydrogen bond lattice that hinders the rotation of His64 at neutral pH. This hydrogen-bond lattice disappears at low pH. Although His64 rotates out of the distal pocket in the MbCO structure at pH 4, leaving more space for the CO ligand, the Fe-C-O angle refines to about 130 degrees, the same as those at pH 5 and 6. In the MbCO structure at pH 4, significant conformational changes appear in the EF corner. The peptide plane between Lys79(EF2) and Gly80(EF3) flips about 150 degrees. The occupancy of this conformation in the MbCO structures increases with decreases in pH. On the proximal side of the heme, the bond between the heme iron atom and N(epsilon) of His93 remains intact under the experimental conditions in the MbCO and deoxyMb structures, but appears elongated in the metMb structure at pH 4, representing either a weakened bond or the breakage of the bond in some fraction of the molecules in the crystal.
+[[Category: Large Structures]]
-==About this Structure==
-VXC 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=1VXC OCA].
-==Reference==
-Crystal structures of CO-, deoxy- and met-myoglobins at various pH values., Yang F, Phillips GN Jr, J Mol Biol. 1996 Mar 8;256(4):762-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8642596 8642596]
 [[Category: Physeter catodon]]
-[[Category: Single protein]]
+[[Category: Phillips Jr GN]]
-[[Category: Jr., G N.Phillips.]]
+[[Category: Yang F]]
-[[Category: Yang, F.]]
-[[Category: Conformational change]]
-[[Category: Oxygen storage]]
-[[Category: Ph value]]
-[[Category: Sperm whale myoglobin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 12:54:08 2008''