3hb3

From Proteopedia

(Difference between revisions)

Revision as of 07:19, 6 September 2023

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase

Structural highlights

3hb3 is a 4 chain structure with sequence from Mus musculus and Paracoccus denitrificans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HVM54_MOUSE

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

The structure of the two-subunit cytochrome c oxidase from Paracoccus denitrificans has been refined using X-ray cryodata to 2.25 A resolution in order to gain further insights into its mechanism of action. The refined structural model shows a number of new features including many additional solvent and detergent molecules. The electron density bridging the heme a(3) iron and Cu(B) of the active site is fitted best by a peroxo-group or a chloride ion. Two waters or OH(-) groups do not fit, one water (or OH(-)) does not provide sufficient electron density. The analysis of crystals of cytochrome c oxidase isolated in the presence of bromide instead of chloride appears to exclude chloride as the bridging ligand. In the D-pathway a hydrogen bonded chain of six water molecules connects Asn131 and Glu278, but the access for protons to this water chain is blocked by Asn113, Asn131 and Asn199. The K-pathway contains two firmly bound water molecules, an additional water chain seems to form its entrance. Above the hemes a cluster of 13 water molecules is observed which potentially form multiple exit pathways for pumped protons. The hydrogen bond pattern excludes that the Cu(B) ligand His326 is present in the imidazolate form.

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways.,Koepke J, Olkhova E, Angerer H, Muller H, Peng G, Michel H Biochim Biophys Acta. 2009 Jun;1787(6):635-45. Epub 2009 Apr 15. PMID:19374884^[1]

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

References

↑ Koepke J, Olkhova E, Angerer H, Muller H, Peng G, Michel H. High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. Biochim Biophys Acta. 2009 Jun;1787(6):635-45. Epub 2009 Apr 15. PMID:19374884 doi:10.1016/j.bbabio.2009.04.003

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hb3"

@@ Line 3: / Line 3: @@
 <StructureSection load='3hb3' size='340' side='right'caption='[[3hb3]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hb3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741] and [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HB3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hb3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HB3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</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]] 2.25&#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;'>[[1ar1|1ar1]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ctaDII ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266 ATCC 17741]), ctaC, coiI, ctaB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266 ATCC 17741])</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=3hb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hb3 OCA], [https://pdbe.org/3hb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hb3 RCSB], [https://www.ebi.ac.uk/pdbsum/3hb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hb3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/COX1B_PARDE COX1B_PARDE]] Subunit 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). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. [[https://www.uniprot.org/uniprot/COX2_PARDE COX2_PARDE]] 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/HVM54_MOUSE HVM54_MOUSE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 40: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 17741]]
-[[Category: Cytochrome-c oxidase]]
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Angerer, H]]
+[[Category: Paracoccus denitrificans]]
-[[Category: Koepke, J]]
+[[Category: Angerer H]]
-[[Category: Peng, G]]
+[[Category: Koepke J]]
-[[Category: Cell inner membrane]]
+[[Category: Peng G]]
-[[Category: Cell membrane]]
-[[Category: Copper]]
-[[Category: Disulfide bond]]
-[[Category: Electron transfer]]
-[[Category: Electron transport]]
-[[Category: Heme]]
-[[Category: Hydrogen ion transport]]
-[[Category: Ion transport]]
-[[Category: Iron]]
-[[Category: Membrane]]
-[[Category: Membrane protein]]
-[[Category: Metal-binding]]
-[[Category: Oxidoreductase]]
-[[Category: Proton pumping]]
-[[Category: Proton transfer]]
-[[Category: Pyrrolidone carboxylic acid]]
-[[Category: Respiratory chain]]
-[[Category: Transmembrane]]
-[[Category: Transport]]

3hb3

From Proteopedia

Revision as of 07:19, 6 September 2023

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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