3eh4: Difference between revisions

Latest revision as of 09:13, 13 August 2026

Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus

Structural highlights

3eh4 is a 3 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	BNG, CU1, CUA, HEM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

COX1_THET8

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

Three paths for obtaining crystals of reduced (II-E4Q/I-K258R) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 A resolution. Microspectrophotometry of single crystals of Thermus ba(3) oxidase at 100 K was used to show that crystals of the oxidized enzyme are reduced in an intense X-ray (beam line 7-1 at the Stanford Synchrotron Radiation Laboratory), being nearly complete in 1 min. The previously reported structures of ba(3) (Protein Data Bank entries 1EHK and 1XME ), having a crystallographically detectable water between the Cu(B) and Fe(a3) metals of the dinuclear center, actually represent the X-ray radiation-reduced enzyme. Dithionite-reduced crystals or crystals formed from dithionite-reduced enzyme revealed the absence of the above-mentioned water and an increase in the Cu(B)-Fe(a3) distance of approximately 0.3 A. The new structures are discussed in terms of enzyme function. An unexpected optical absorption envelope at approximately 590 nm is also reported. This spectral feature is tentatively thought to arise from a five-coordinate, low-spin, ferrous heme a(3) that is trapped in the frozen crystals.

Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme.,Liu B, Chen Y, Doukov T, Soltis SM, Stout CD, Fee JA Biochemistry. 2009 Feb 10;48(5):820-6. PMID:19140675^[1]

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

References

↑ Liu B, Chen Y, Doukov T, Soltis SM, Stout CD, Fee JA. Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Biochemistry. 2009 Feb 10;48(5):820-6. PMID:19140675 doi:10.1021/bi801759a

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Liu B, Chen Y, Doukov T, Soltis SM, Stout CD, Fee JA. Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Biochemistry. 2009 Feb 10;48(5):820-6. PMID:19140675 doi:10.1021/bi801759a

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='3eh4' size='340' side='right'caption='[[3eh4]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3eh4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EH4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3eh4]] 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=3EH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EH4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</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></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]] 2.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qpd|2qpd]], [[2qpe|2qpe]], [[1xme|1xme]], [[3eh3|3eh3]], [[3eh5|3eh5]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cbaA, TTHA1135 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbaB, ctaC, TTHA1134 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbaD, TTHA1133 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3eh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eh4 OCA], [https://pdbe.org/3eh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eh4 RCSB], [https://www.ebi.ac.uk/pdbsum/3eh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eh4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://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]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eh/3eh4_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 38: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Cytochrome-c oxidase]]
 [[Category: Large Structures]]
-[[Category: Thet8]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Chen, Y]]
+[[Category: Chen Y]]
-[[Category: Doukov, T]]
+[[Category: Doukov T]]
-[[Category: Fee, J A]]
+[[Category: Fee JA]]
-[[Category: Liu, B]]
+[[Category: Liu B]]
-[[Category: Soltis, S M]]
+[[Category: Soltis SM]]
-[[Category: Stout, D]]
+[[Category: Stout D]]
-[[Category: Cell membrane]]
-[[Category: Copper]]
-[[Category: Cytochrome ba3 oxidase]]
-[[Category: Electron transport]]
-[[Category: Formylation]]
-[[Category: Heme]]
-[[Category: Hydrogen ion transport]]
-[[Category: Integral membrane protein]]
-[[Category: Ion transport]]
-[[Category: Iron]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Respiratory chain]]
-[[Category: Transmembrane]]
-[[Category: Transport]]

3eh4: Difference between revisions

Latest revision as of 09:13, 13 August 2026

Structure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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