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PDBsum entry 3m9c

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
3m9c
Jmol
Contents
Protein chains
474 a.a.
391 a.a.
281 a.a.
PDB id:
3m9c
Name: Oxidoreductase
Title: Crystal structure of the membrane domain of respiratory comp escherichia coli
Structure: Nadh-quinone oxidoreductase subunit nuol. Chain: l. Fragment: membrane domain. Mutation: yes. Nadh-quinone oxidoreductase subunit nuom. Chain: m. Fragment: membrane domain. Mutation: yes. Nadh-quinone oxidoreductase subunit nuon.
Source: Escherichia coli. Organism_taxid: 562. Strain: bl21. Strain: bl21
Resolution:
3.90Å     R-factor:   not given    
Authors: R.G.Efremov,R.Baradaran,L.A.Sazanov
Key ref: R.G.Efremov et al. (2010). The architecture of respiratory complex I. Nature, 465, 441-445. PubMed id: 20505720
Date:
22-Mar-10     Release date:   26-May-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 474 a.a.
Protein chains
No UniProt id for this chain
Struc: 391 a.a.
Protein chain
No UniProt id for this chain
Struc: 281 a.a.
Key:    Secondary structure

 Enzyme reactions 
   Enzyme class: Chains L, M, N, R: E.C.1.6.5.3  - NADH:ubiquinone reductase (H(+)-translocating).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADH + ubiquinone + 5 H+(In) = NAD+ + ubiquinol + 4 H(+)(Out)
NADH
+ ubiquinone
+ 5 × H(+)(In)
= NAD(+)
+ ubiquinol
+ 4 × H(+)(Out)
      Cofactor: FMN; Iron-sulfur
FMN
Iron-sulfur
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Nature 465:441-445 (2010)
PubMed id: 20505720  
 
 
The architecture of respiratory complex I.
R.G.Efremov, R.Baradaran, L.A.Sazanov.
 
  ABSTRACT  
 
Complex I is the first enzyme of the respiratory chain and has a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation by an unknown mechanism. Dysfunction of complex I has been implicated in many human neurodegenerative diseases. We have determined the structure of its hydrophilic domain previously. Here, we report the alpha-helical structure of the membrane domain of complex I from Escherichia coli at 3.9 A resolution. The antiporter-like subunits NuoL/M/N each contain 14 conserved transmembrane (TM) helices. Two of them are discontinuous, as in some transporters. Unexpectedly, subunit NuoL also contains a 110-A long amphipathic alpha-helix, spanning almost the entire length of the domain. Furthermore, we have determined the structure of the entire complex I from Thermus thermophilus at 4.5 A resolution. The L-shaped assembly consists of the alpha-helical model for the membrane domain, with 63 TM helices, and the known structure of the hydrophilic domain. The architecture of the complex provides strong clues about the coupling mechanism: the conformational changes at the interface of the two main domains may drive the long amphipathic alpha-helix of NuoL in a piston-like motion, tilting nearby discontinuous TM helices, resulting in proton translocation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23417064 R.Baradaran, J.M.Berrisford, G.S.Minhas, and L.A.Sazanov (2013).
Crystal structure of the entire respiratory complex I.
  Nature, 494, 443-448.
PDB codes: 4he8 4hea
23151580 S.B.Vafai, and V.K.Mootha (2012).
Mitochondrial disorders as windows into an ancient organelle.
  Nature, 491, 374-383.  
21265782 C.Bricio, L.Alvarez, M.J.Gómez, and J.Berenguer (2011).
Partial and complete denitrification in Thermus thermophilus: lessons from genome drafts.
  Biochem Soc Trans, 39, 249-253.  
21822288 R.G.Efremov, and L.A.Sazanov (2011).
Structure of the membrane domain of respiratory complex I.
  Nature, 476, 414-420.
PDB code: 3rko
21226204 R.Hielscher, T.Friedrich, and P.Hellwig (2011).
Far- and mid-infrared spectroscopic analysis of the substrate-induced structural dynamics of respiratory complex I.
  Chemphyschem, 12, 217-224.  
21420404 S.B.Vik (2011).
The transmembrane helices of the L, M, and N subunits of Complex I from E. coli can be assigned on the basis of conservation and hydrophobic moment analysis.
  FEBS Lett, 585, 1180-1184.  
21150889 S.J.Hoefs, F.J.van Spronsen, E.W.Lenssen, L.G.Nijtmans, R.J.Rodenburg, J.A.Smeitink, and L.P.van den Heuvel (2011).
NDUFA10 mutations cause complex I deficiency in a patient with Leigh disease.
  Eur J Hum Genet, 19, 270-274.  
21464825 T.A.Krulwich, G.Sachs, and E.Padan (2011).
Molecular aspects of bacterial pH sensing and homeostasis.
  Nat Rev Microbiol, 9, 330-343.  
21120593 B.Amarneh, and S.B.Vik (2010).
Transmembrane topology of subunit N of complex I (NADH:ubiquinone oxidoreductase) from Escherichia coli.
  J Bioenerg Biomembr, 42, 511-516.  
20818725 D.C.Wallace (2010).
Bioenergetics and the epigenome: interface between the environment and genes in common diseases.
  Dev Disabil Res Rev, 16, 114-119.  
20679390 D.C.Wallace (2010).
The epigenome and the mitochondrion: bioenergetics and the environment [corrected].
  Genes Dev, 24, 1571-1573.  
20858599 E.Fassone, A.J.Duncan, J.W.Taanman, A.T.Pagnamenta, M.I.Sadowski, T.Holand, W.Qasim, P.Rutland, S.E.Calvo, V.K.Mootha, M.Bitner-Glindzicz, and S.Rahman (2010).
FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy.
  Hum Mol Genet, 19, 4837-4847.  
20818732 F.Valsecchi, W.J.Koopman, G.R.Manjeri, R.J.Rodenburg, J.A.Smeitink, and P.H.Willems (2010).
Complex I disorders: causes, mechanisms, and development of treatment strategies at the cellular level.
  Dev Disabil Res Rev, 16, 175-182.  
20818735 S.L.Rea, B.H.Graham, E.Nakamaru-Ogiso, A.Kar, and M.J.Falk (2010).
Bacteria, yeast, worms, and flies: exploiting simple model organisms to investigate human mitochondrial diseases.
  Dev Disabil Res Rev, 16, 200-218.  
20974925 T.Hayashi, and A.A.Stuchebrukhov (2010).
Electron tunneling in respiratory complex I.
  Proc Natl Acad Sci U S A, 107, 19157-19162.  
20505714 T.Ohnishi (2010).
Structural biology: Piston drives a proton pump.
  Nature, 465, 428-429.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.