This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3s39

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:44, 14 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Structure of Thermus thermophilus cytochrome ba3 oxidase 60s after Xe depressurization==
==Structure of Thermus thermophilus cytochrome ba3 oxidase 60s after Xe depressurization==
-
<StructureSection load='3s39' size='340' side='right' caption='[[3s39]], [[Resolution|resolution]] 4.80&Aring;' scene=''>
+
<StructureSection load='3s39' size='340' side='right'caption='[[3s39]], [[Resolution|resolution]] 4.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3s39]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S39 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3s39]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S39 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4.8&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3s33|3s33]], [[3s38|3s38]], [[3s3a|3s3a]], [[3s3b|3s3b]], [[3s3c|3s3c]], [[3s3d|3s3d]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cbaa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbab, cbac ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbad ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</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=3s39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s39 OCA], [https://pdbe.org/3s39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s39 RCSB], [https://www.ebi.ac.uk/pdbsum/3s39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s39 ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>
+
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s39 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s39 RCSB], [http://www.ebi.ac.uk/pdbsum/3s39 PDBsum]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/COX2_THET8 COX2_THET8]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
+
[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8]
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
We use a form of "freeze-trap, kinetic-crystallography" to explore the migration of Xe atoms away from the dinuclear heme-a3/CuB center in Thermus thermophilus cytochrome ba3 oxidase. This enzyme is a member of the heme-copper oxidase super-family, and is thus crucial for dioxygen dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O2 diffusion channel in cytochrome ba3 oxidase that is continuous, Y-shaped, 18-20 A in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a3-CuB center in the active site. To understand movement of gas molecules within the O2 channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 seconds while undergoing out-gassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 --&gt; Xe5 --&gt; Xe3 --&gt; Xe4 sites, suggesting that ingress of O2 is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.
+
-
 
+
-
Mobility of Xe atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase.,Luna VM, Fee JA, Deniz AA, Stout CD Biochemistry. 2012 May 19. PMID:22607023<ref>PMID:22607023</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
-
*[[Cytochrome c oxidase|Cytochrome c oxidase]]
+
*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Cytochrome-c oxidase]]
+
[[Category: Large Structures]]
-
[[Category: Thermus thermophilus]]
+
[[Category: Thermus thermophilus HB8]]
-
[[Category: Deniz, A A]]
+
[[Category: Deniz AA]]
-
[[Category: Fee, J A]]
+
[[Category: Fee JA]]
-
[[Category: Luna, V M]]
+
[[Category: Luna VM]]
-
[[Category: Stout, C D]]
+
[[Category: Stout CD]]
-
[[Category: Oxidoreductase]]
+
-
[[Category: Xenon]]
+

Current revision

Structure of Thermus thermophilus cytochrome ba3 oxidase 60s after Xe depressurization

PDB ID 3s39

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3s39"
Personal tools