2r4z: Difference between revisions

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New page: left|200px<br /><applet load="2r4z" size="350" color="white" frame="true" align="right" spinBox="true" caption="2r4z, resolution 1.60Å" /> '''Ligand Migration and...
 
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[[Image:2r4z.jpg|left|200px]]<br /><applet load="2r4z" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2r4z, resolution 1.60&Aring;" />
'''Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO'''<br />


==Overview==
==Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO==
Using Fourier transform infrared (FTIR) spectroscopy combined with, temperature derivative spectroscopy (TDS) at cryogenic temperatures, we, have studied CO binding to the heme and CO migration among cavities in the, interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after, photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking, site B in close vicinity to the heme iron, and two secondary docking sites, C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess, the relevance of these findings for physiological binding, we also, performed flash photolysis experiments on HbICO at room temperature and, equilibrium binding studies with dioxygen. Our results show that the Xe4, and Xe2 cavities serve as transient docking sites for unbound ligands in, the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears, as a plausible entry/exit route as well.
<StructureSection load='2r4z' size='340' side='right'caption='[[2r4z]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2r4z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anadara_inaequivalvis Anadara inaequivalvis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R4Z 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]] 1.6&#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=PO4:PHOSPHATE+ION'>PO4</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=2r4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r4z OCA], [https://pdbe.org/2r4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r4z RCSB], [https://www.ebi.ac.uk/pdbsum/2r4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r4z ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GLB1_ANAIN GLB1_ANAIN]
== 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/r4/2r4z_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=2r4z ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.


==About this Structure==
Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis.,Nienhaus K, Knapp JE, Palladino P, Royer WE Jr, Nienhaus GU Biochemistry. 2007 Dec 11;46(49):14018-31. Epub 2007 Nov 15. PMID:18001141<ref>PMID:18001141</ref>
2R4Z is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=HEM:'>HEM</scene> and <scene name='pdbligand=CMO:'>CMO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R4Z OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca inaequivalvis(,)., Nienhaus K, Knapp JE, Palladino P, Royer WE Jr, Nienhaus GU, Biochemistry. 2007 Nov 15;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18001141 18001141]
</div>
[[Category: Scapharca inaequivalvis]]
<div class="pdbe-citations 2r4z" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
[[Category: Jr., W.E.Royer.]]
[[Category: Knapp, J.E.]]
[[Category: Nienhaus, G.U.]]
[[Category: Nienhaus, K.]]
[[Category: Palladino, P.]]
[[Category: CMO]]
[[Category: HEM]]
[[Category: PO4]]
[[Category: allostery]]
[[Category: cytoplasm]]
[[Category: heme]]
[[Category: iron]]
[[Category: metal-binding]]
[[Category: oxygen affinity]]
[[Category: oxygen binding]]
[[Category: oxygen storage/transport]]
[[Category: oxygen transport]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:31:57 2008''
==See Also==
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Anadara inaequivalvis]]
[[Category: Large Structures]]
[[Category: Knapp JE]]
[[Category: Nienhaus GU]]
[[Category: Nienhaus K]]
[[Category: Palladino P]]
[[Category: Royer Jr WE]]

Latest revision as of 12:03, 25 October 2023

Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with COLigand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: Structure of I25W with CO

Structural highlights

2r4z is a 2 chain structure with sequence from Anadara inaequivalvis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLB1_ANAIN

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 PubMed

Using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures, we have studied CO binding to the heme and CO migration among cavities in the interior of the dimeric hemoglobin of Scapharca inaequivalvis (HbI) after photodissociation. By combining these studies with X-ray crystallography, three transient ligand docking sites were identified: a primary docking site B in close vicinity to the heme iron, and two secondary docking sites C and D corresponding to the Xe4 and Xe2 cavities of myoglobin. To assess the relevance of these findings for physiological binding, we also performed flash photolysis experiments on HbICO at room temperature and equilibrium binding studies with dioxygen. Our results show that the Xe4 and Xe2 cavities serve as transient docking sites for unbound ligands in the protein, but not as way stations on the entry/exit pathway. For HbI, the so-called histidine gate mechanism proposed for other globins appears as a plausible entry/exit route as well.

Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis.,Nienhaus K, Knapp JE, Palladino P, Royer WE Jr, Nienhaus GU Biochemistry. 2007 Dec 11;46(49):14018-31. Epub 2007 Nov 15. PMID:18001141[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Nienhaus K, Knapp JE, Palladino P, Royer WE Jr, Nienhaus GU. Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis. Biochemistry. 2007 Dec 11;46(49):14018-31. Epub 2007 Nov 15. PMID:18001141 doi:10.1021/bi7016798

2r4z, resolution 1.60Å

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