6rko

From Proteopedia

(Difference between revisions)

Revision as of 08:09, 23 October 2019

Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution

Structural highlights

6rko is a 4 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Gene:	cydB, cyd-2, b0734, JW0723 (ECOLI), cydA, cyd-1, b0733, JW0722 (ECOLI), ynhF, b4602, JW1649.1 (ECOLI), cydX, ybgT, b4515, JW0724 (ECOLI)
Activity:	Ubiquinol oxidase (electrogenic, proton-motive force generating), with EC number 7.1.1.7
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CYDX_ECOLI] Required for correct functioning of cytochrome bd-I oxidase. This protein and AppX may have some functional overlap. [CYDB_ECOLI] A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.^[1] ^[2] ^[3] [CYDA_ECOLI] A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.^[4] ^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of the Escherichia coli cytochrome bd-I oxidase by single-particle cryo-electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily-specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases.,Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kuhlbrandt W, Michel H Science. 2019 Oct 4;366(6461):100-104. doi: 10.1126/science.aay0967. PMID:31604309^[9]

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

References

↑ Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ. Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol. 2009 Sep;191(17):5510-7. doi: 10.1128/JB.00562-09. Epub 2009 Jun 19. PMID:19542282 doi:http://dx.doi.org/10.1128/JB.00562-09
↑ Borisov VB, Murali R, Verkhovskaya ML, Bloch DA, Han H, Gennis RB, Verkhovsky MI. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17320-4. doi:, 10.1073/pnas.1108217108. Epub 2011 Oct 10. PMID:21987791 doi:http://dx.doi.org/10.1073/pnas.1108217108
↑ Miller MJ, Gennis RB. The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain. J Biol Chem. 1983 Aug 10;258(15):9159-65. PMID:6307994
↑ Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ. Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol. 2009 Sep;191(17):5510-7. doi: 10.1128/JB.00562-09. Epub 2009 Jun 19. PMID:19542282 doi:http://dx.doi.org/10.1128/JB.00562-09
↑ Borisov VB, Murali R, Verkhovskaya ML, Bloch DA, Han H, Gennis RB, Verkhovsky MI. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17320-4. doi:, 10.1073/pnas.1108217108. Epub 2011 Oct 10. PMID:21987791 doi:http://dx.doi.org/10.1073/pnas.1108217108
↑ Fang H, Lin RJ, Gennis RB. Location of heme axial ligands in the cytochrome d terminal oxidase complex of Escherichia coli determined by site-directed mutagenesis. J Biol Chem. 1989 May 15;264(14):8026-32. PMID:2656671
↑ Miller MJ, Gennis RB. The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain. J Biol Chem. 1983 Aug 10;258(15):9159-65. PMID:6307994
↑ Kaysser TM, Ghaim JB, Georgiou C, Gennis RB. Methionine-393 is an axial ligand of the heme b558 component of the cytochrome bd ubiquinol oxidase from Escherichia coli. Biochemistry. 1995 Oct 17;34(41):13491-501. doi: 10.1021/bi00041a029. PMID:7577938 doi:http://dx.doi.org/10.1021/bi00041a029
↑ Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kuhlbrandt W, Michel H. Active site rearrangement and structural divergence in prokaryotic respiratory oxidases. Science. 2019 Oct 4;366(6461):100-104. doi: 10.1126/science.aay0967. PMID:31604309 doi:http://dx.doi.org/10.1126/science.aay0967

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6rko"

@@ Line 3: / Line 3: @@
 <StructureSection load='6rko' size='340' side='right'caption='[[6rko]], [[Resolution|resolution]] 2.68&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6rko]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RKO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6rko]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RKO FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene>, <scene name='pdbligand=HEB:HEME+B/C'>HEB</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=POV:(2S)-3-(HEXADECANOYLOXY)-2-[(9Z)-OCTADEC-9-ENOYLOXY]PROPYL+2-(TRIMETHYLAMMONIO)ETHYL+PHOSPHATE'>POV</scene>, <scene name='pdbligand=UQ8:UBIQUINONE-8'>UQ8</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cydB, cyd-2, b0734, JW0723 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), cydA, cyd-1, b0733, JW0722 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), ynhF, b4602, JW1649.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), cydX, ybgT, b4515, JW0724 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquinol_oxidase_(electrogenic,_proton-motive_force_generating) Ubiquinol oxidase (electrogenic, proton-motive force generating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.1.1.7 7.1.1.7] </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=6rko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rko OCA], [http://pdbe.org/6rko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rko RCSB], [http://www.ebi.ac.uk/pdbsum/6rko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rko ProSAT]</span></td></tr>
@@ Line 10: / Line 11: @@
 == Function ==
 [[http://www.uniprot.org/uniprot/CYDX_ECOLI CYDX_ECOLI]] Required for correct functioning of cytochrome bd-I oxidase. This protein and AppX may have some functional overlap. [[http://www.uniprot.org/uniprot/CYDB_ECOLI CYDB_ECOLI]] A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.<ref>PMID:19542282</ref> <ref>PMID:21987791</ref> <ref>PMID:6307994</ref>  [[http://www.uniprot.org/uniprot/CYDA_ECOLI CYDA_ECOLI]] A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.<ref>PMID:19542282</ref> <ref>PMID:21987791</ref> <ref>PMID:2656671</ref> <ref>PMID:6307994</ref> <ref>PMID:7577938</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cytochrome bd-type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of the Escherichia coli cytochrome bd-I oxidase by single-particle cryo-electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily-specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.
+Active site rearrangement and structural divergence in prokaryotic respiratory oxidases.,Safarian S, Hahn A, Mills DJ, Radloff M, Eisinger ML, Nikolaev A, Meier-Credo J, Melin F, Miyoshi H, Gennis RB, Sakamoto J, Langer JD, Hellwig P, Kuhlbrandt W, Michel H Science. 2019 Oct 4;366(6461):100-104. doi: 10.1126/science.aay0967. PMID:31604309<ref>PMID:31604309</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6rko" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Ecoli]]
 [[Category: Large Structures]]
 [[Category: Hahn, A]]

6rko

From Proteopedia

Revision as of 08:09, 23 October 2019

Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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