2vyy: Difference between revisions

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-{{Seed}}
-[[Image:2vyy.png|left|200px]]
-<!--
+==Mutant Ala55Trp of Cerebratuls lacteus mini-hemoglobin==
-The line below this paragraph, containing "STRUCTURE_2vyy", creates the "Structure Box" on the page.
+<StructureSection load='2vyy' size='340' side='right'caption='[[2vyy]], [[Resolution|resolution]] 1.60&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'>[[2vyy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cerebratulus_lacteus Cerebratulus lacteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VYY 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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>
-{{STRUCTURE_2vyy|  PDB=2vyy  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vyy OCA], [https://pdbe.org/2vyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vyy RCSB], [https://www.ebi.ac.uk/pdbsum/2vyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vyy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLBN_CERLA GLBN_CERLA] Acts as an oxygen store capable of sustaining neuronal activity in an anoxic environment for 5 to 30 min.
+== 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/vy/2vyy_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=2vyy ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The major pathway for O2 binding to mammalian myoglobins (Mb) and hemoglobins (Hb) involves transient upward movement of the distal histidine (His-64(E7)), allowing ligand capture in the distal pocket. The mini-globin from Cerebratulus lacteus (CerHb) appears to have an alternative pathway between the E and H helices that is made accessible by loss of the N-terminal A helix. To test this pathway, we examined the effects of changing the size of the E7 gate and closing the end of the apolar channel in CerHb by site-directed mutagenesis. Increasing the size of Gln-44(E7) from Ala to Trp causes variation of association (k'O2) and dissociation (kO2) rate coefficients, but the changes are not systematic. More significantly, the fractions (Fgem approximately 0.05-0.19) and rates (kgem approximately 50-100 micros(-1)) of geminate CO recombination in the Gln-44(E7) mutants are all similar. In contrast, blocking the entrance to the apolar channel by increasing the size of Ala-55(E18) to Phe and Trp causes the following: 1) both k'O2 and kO2 to decrease roughly 4-fold; 2) Fgem for CO to increase from approximately 0.05 to 0.45; and 3) kgem to decrease from approximately 80 to approximately 9 micros(-1), as ligands become trapped in the channel. Crystal structures and low temperature Fourier-transform infrared spectra of Phe-55 and Trp-55 CerHb confirm that the aromatic side chains block the channel entrance, with little effect on the distal pocket. These results provide unambiguous experimental proof that diatomic ligands can enter and exit a globin through an interior channel in preference to the more direct E7 pathway.
-===MUTANT ALA55TRP OF CEREBRATULS LACTEUS MINI-HEMOGLOBIN===
+The apolar channel in Cerebratulus lacteus hemoglobin is the route for O2 entry and exit.,Salter MD, Nienhaus K, Nienhaus GU, Dewilde S, Moens L, Pesce A, Nardini M, Bolognesi M, Olson JS J Biol Chem. 2008 Dec 19;283(51):35689-702. Epub 2008 Oct 7. PMID:18840607<ref>PMID:18840607</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vyy" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18840607}}, adds the Publication Abstract to the page
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18840607 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18840607}}
+__TOC__
+</StructureSection>
-==About this Structure==
-VYY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Cerebratulus_lacteus Cerebratulus lacteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VYY OCA].
-==Reference==
-The Apolar Channel in Cerebratulus lacteus Hemoglobin Is the Route for O2 Entry and Exit., Salter MD, Nienhaus K, Nienhaus GU, Dewilde S, Moens L, Pesce A, Nardini M, Bolognesi M, Olson JS, J Biol Chem. 2008 Dec 19;283(51):35689-702. Epub 2008 Oct 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18840607 18840607]
 [[Category: Cerebratulus lacteus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Bolognesi M]]
-[[Category: Ala55trp mutant]]
+[[Category: Dewilde S]]
-[[Category: Heme]]
+[[Category: Moens L]]
-[[Category: Iron]]
+[[Category: Nardini M]]
-[[Category: Metal-binding]]
+[[Category: Nienhaus GU]]
-[[Category: Mini-hemoglobin]]
+[[Category: Nienhaus K]]
-[[Category: Oxygen transport]]
+[[Category: Olson JS]]
-[[Category: Transport]]
+[[Category: Pesce A]]
+[[Category: Salter MD]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 24 20:50:07 2008''