1i4y: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
New page: left|200px<br /><applet load="1i4y" size="450" color="white" frame="true" align="right" spinBox="true" caption="1i4y, resolution 1.80Å" /> '''THE CRYSTAL STRUCTUR...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1i4y.jpg|left|200px]]<br /><applet load="1i4y" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1i4y, resolution 1.80&Aring;" />
'''THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII WILD TYPE METHEMERYTHRIN'''<br />


==Overview==
==THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII WILD TYPE METHEMERYTHRIN==
Reported are the X-ray crystal structures of recombinant Phascolopsis, gouldii methemerythrin (1.8-A resolution) and the structure of an, O2-binding-pocket mutant, L98Y methemerythrin (2.1-A resolution). The L98Y, hemerythrin (Hr) has a greatly enhanced O2 affinity, a slower O2, dissociation rate, a larger solvent deuterium isotope effect on this rate, and a greater resistance to autoxidation relative to the wild-type, protein. The crystal structures show that the hydrophobic binding pocket, of Hr can accommodate substitution of a leucyl by a tyrosyl side chain, with relatively minor structural rearrangements. UV/vis and resonance, Raman spectra show that in solution L98Y methemerythrin contains a mixture, of two diiron site structures differing by the absence or presence of an, Fe(III)-coordinated phenolate. However, in the crystal, only one L98Y, diiron site structure is seen, in which the Y98 hydroxyl is not a ligand, but instead forms a hydrogen bond to a terminal hydroxo/aqua ligand to the, nearest iron. Based on this crystal structure, we propose that in the oxy, form of L98Y hemerythrin the non-polar nature of the binding pocket favors, localization of the Y98 hydroxyl near the O2 binding site, where it can, donate a hydrogen bond to the hydroperoxo ligand. The stabilizing, Y98OH-O2H-interaction would account for all of the altered O2 binding, properties of L98Y Hr listed above.
<StructureSection load='1i4y' size='340' side='right'caption='[[1i4y]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1i4y]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Phascolopsis_gouldii Phascolopsis gouldii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I4Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I4Y 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]] 1.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</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=1i4y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i4y OCA], [https://pdbe.org/1i4y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i4y RCSB], [https://www.ebi.ac.uk/pdbsum/1i4y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i4y ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HEMT_PHAGO HEMT_PHAGO] Hemerythrin is a respiratory protein in blood cells of certain marine worms. The oxygen-binding site in each chain contains two iron atoms.
== 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/i4/1i4y_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1i4y ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Reported are the X-ray crystal structures of recombinant Phascolopsis gouldii methemerythrin (1.8-A resolution) and the structure of an O2-binding-pocket mutant, L98Y methemerythrin (2.1-A resolution). The L98Y hemerythrin (Hr) has a greatly enhanced O2 affinity, a slower O2 dissociation rate, a larger solvent deuterium isotope effect on this rate, and a greater resistance to autoxidation relative to the wild-type protein. The crystal structures show that the hydrophobic binding pocket of Hr can accommodate substitution of a leucyl by a tyrosyl side chain with relatively minor structural rearrangements. UV/vis and resonance Raman spectra show that in solution L98Y methemerythrin contains a mixture of two diiron site structures differing by the absence or presence of an Fe(III)-coordinated phenolate. However, in the crystal, only one L98Y diiron site structure is seen, in which the Y98 hydroxyl is not a ligand, but instead forms a hydrogen bond to a terminal hydroxo/aqua ligand to the nearest iron. Based on this crystal structure, we propose that in the oxy form of L98Y hemerythrin the non-polar nature of the binding pocket favors localization of the Y98 hydroxyl near the O2 binding site, where it can donate a hydrogen bond to the hydroperoxo ligand. The stabilizing Y98OH-O2H-interaction would account for all of the altered O2 binding properties of L98Y Hr listed above.


==About this Structure==
The crystal structures of Phascolopsis gouldii wild type and L98Y methemerythrins: structural and functional alterations of the O2 binding pocket.,Farmer CS, Kurtz DM Jr, Liu ZJ, Wang BC, Rose J, Ai J, Sanders-Loehr J J Biol Inorg Chem. 2001 Apr;6(4):418-29. PMID:11372200<ref>PMID:11372200</ref>
1I4Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Phascolopsis_gouldii Phascolopsis gouldii] with CL and FEO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1I4Y OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The crystal structures of Phascolopsis gouldii wild type and L98Y methemerythrins: structural and functional alterations of the O2 binding pocket., Farmer CS, Kurtz DM Jr, Liu ZJ, Wang BC, Rose J, Ai J, Sanders-Loehr J, J Biol Inorg Chem. 2001 Apr;6(4):418-29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11372200 11372200]
</div>
<div class="pdbe-citations 1i4y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Phascolopsis gouldii]]
[[Category: Phascolopsis gouldii]]
[[Category: Single protein]]
[[Category: Farmer CS]]
[[Category: Farmer, C.S.]]
[[Category: Kurtz Jr DM]]
[[Category: Jr., D.M.Kurtz.]]
[[Category: Liu Z-J]]
[[Category: Liu, Z.J.]]
[[Category: Rose J]]
[[Category: Rose, J.]]
[[Category: Wang BC]]
[[Category: Wang, B.C.]]
[[Category: CL]]
[[Category: FEO]]
[[Category: diiron]]
[[Category: four-helix bundle]]
[[Category: hemerythrin]]
[[Category: oxygen binding]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:03:17 2007''
Retrieved from "https://proteopedia.org/1i4y"