3iam

From Proteopedia

(Difference between revisions)

Revision as of 19:40, 24 December 2014

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH

Structural highlights

3iam is a 16 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Related:	2fug, 3i9v, 3ias
Activity:	NADH dehydrogenase (quinone), with EC number 1.6.99.5
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[NQO6_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [NQO3_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. [NQO9_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [NQO2_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. [NQO15_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.^[1] [NQO1_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [NQO4_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [NQO5_THET8] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]

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

Complex I plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. The mechanism of this highly efficient enzyme is currently unknown. Mitochondrial complex I is a major source of reactive oxygen species, which may be one of the causes of aging. Dysfunction of complex I is implicated in many human neurodegenerative diseases. We have determined several x-ray structures of the oxidized and reduced hydrophilic domain of complex I from Thermus thermophilus at up to 3.1 A resolution. The structures reveal the mode of interaction of complex I with NADH, explaining known kinetic data and providing implications for the mechanism of reactive oxygen species production at the flavin site of complex I. Bound metals were identified in the channel at the interface with the frataxin-like subunit Nqo15, indicating possible iron-binding sites. Conformational changes upon reduction of the complex involve adjustments in the nucleotide-binding pocket, as well as small but significant shifts of several alpha-helices at the interface with the membrane domain. These shifts are likely to be driven by the reduction of nearby iron-sulfur clusters N2 and N6a/b. Cluster N2 is the electron donor to quinone and is coordinated by unique motif involving two consecutive (tandem) cysteines. An unprecedented "on/off switch" (disconnection) of coordinating bonds between the tandem cysteines and this cluster was observed upon reduction. Comparison of the structures suggests a novel mechanism of coupling between electron transfer and proton translocation, combining conformational changes and protonation/deprotonation of tandem cysteines.

Structural basis for the mechanism of respiratory complex I.,Berrisford JM, Sazanov LA J Biol Chem. 2009 Oct 23;284(43):29773-83. Epub 2009 Jul 27. PMID:19635800^[2]

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

References

↑ Sazanov LA, Hinchliffe P. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science. 2006 Mar 10;311(5766):1430-6. Epub 2006 Feb 9. PMID:16469879
↑ Berrisford JM, Sazanov LA. Structural basis for the mechanism of respiratory complex I. J Biol Chem. 2009 Oct 23;284(43):29773-83. Epub 2009 Jul 27. PMID:19635800 doi:10.1074/jbc.M109.032144

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 8: / Line 8: @@
 <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=3iam FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iam OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iam RCSB], [http://www.ebi.ac.uk/pdbsum/3iam PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/NQO6_THET8 NQO6_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP.[HAMAP-Rule:MF_01356] [[http://www.uniprot.org/uniprot/NQO3_THET8 NQO3_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO9_THET8 NQO9_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The role of the nqo9 subunit appears to provide a 'connecting chain' of two clusters between cluster N5 and the terminal cluster N2, and to stabilize the structure of the complex by interacting with other subunits.[HAMAP-Rule:MF_01351] [[http://www.uniprot.org/uniprot/NQO2_THET8 NQO2_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. [[http://www.uniprot.org/uniprot/NQO15_THET8 NQO15_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo15 subunit has probably a role in complex stabilization, and may be also involved in the storage of iron for iron-sulfur cluster regeneration in the complex.<ref>PMID:16469879</ref>  [[http://www.uniprot.org/uniprot/NQO1_THET8 NQO1_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo1 subunit contains the NADH-binding site and the primary electron acceptor FMN. [[http://www.uniprot.org/uniprot/NQO4_THET8 NQO4_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo4 subunit may contain the quinone-binding site.[HAMAP-Rule:MF_01358] [[http://www.uniprot.org/uniprot/NQO5_THET8 NQO5_THET8]] NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP. The nqo5 subunit may be involved in the stabilization of the complex.[HAMAP-Rule:MF_01357]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

3iam

From Proteopedia

Revision as of 19:40, 24 December 2014

Crystal structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus, reduced, 2 mol/ASU, with bound NADH

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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