PDBsum entry 2fug

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
432 a.a. *
178 a.a. *
737 a.a. *
370 a.a. *
191 a.a. *
144 a.a. *
154 a.a. *
127 a.a. *
SF4 ×28
FES ×8
FMN ×4
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of the hydrophilic domain of respiratory c from thermus thermophilus
Structure: Nadh-quinone oxidoreductase chain 1. Chain: 1, a, j, s. Fragment: hydrophilic domain. Synonym: nadh dehydrogenase i, chain 1, ndh-1, chain 1. Nadh-quinone oxidoreductase chain 2. Chain: 2, b, k, t. Synonym: nadh dehydrogenase i, chain 2, ndh-1, chain 2. Nadh-quinone oxidoreductase chain 3. Chain: 3, c, l, u.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Biol. unit: Octamer (from PQS)
3.30Å     R-factor:   0.265     R-free:   0.298
Authors: L.A.Sazanov,P.Hinchliffe
Key ref:
L.A.Sazanov and P.Hinchliffe (2006). Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science, 311, 1430-1436. PubMed id: 16469879 DOI: 10.1126/science.1123809
26-Jan-06     Release date:   14-Feb-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q56222  (NQO1_THET8) -  NADH-quinone oxidoreductase subunit 1
438 a.a.
432 a.a.
Protein chains
Pfam   ArchSchema ?
Q56221  (NQO2_THET8) -  NADH-quinone oxidoreductase subunit 2
181 a.a.
178 a.a.
Protein chains
Pfam   ArchSchema ?
Q56223  (NQO3_THET8) -  NADH-quinone oxidoreductase subunit 3
783 a.a.
737 a.a.
Protein chains
Pfam   ArchSchema ?
Q56220  (NQO4_THET8) -  NADH-quinone oxidoreductase subunit 4
409 a.a.
370 a.a.
Protein chains
Pfam   ArchSchema ?
Q56219  (NQO5_THET8) -  NADH-quinone oxidoreductase subunit 5
207 a.a.
191 a.a.
Protein chains
Pfam   ArchSchema ?
Q56218  (NQO6_THET8) -  NADH-quinone oxidoreductase subunit 6
181 a.a.
144 a.a.
Protein chains
Pfam   ArchSchema ?
Q56224  (NQO9_THET8) -  NADH-quinone oxidoreductase subunit 9
182 a.a.
154 a.a.
Protein chains
Pfam   ArchSchema ?
Q5SKZ7  (NQO15_THET8) -  NADH-quinone oxidoreductase subunit 15
129 a.a.
127 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains 1, 2, 3, 4, 5, 6, 9, 7, A, B, C, D, E, F, G, H, J, K, L, M, N, O, P, Q, S, T, U, V, W, X, Y, Z: E.C.  - Nadh dehydrogenase (quinone).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADH + acceptor = NAD+ + reduced acceptor
Bound ligand (Het Group name = FMN)
matches with 41.51% similarity
+ acceptor
= NAD(+)
+ reduced acceptor
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     electron carrier activity     15 terms  


    Added reference    
DOI no: 10.1126/science.1123809 Science 311:1430-1436 (2006)
PubMed id: 16469879  
Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus.
L.A.Sazanov, P.Hinchliffe.
Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster N1a, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.
  Selected figure(s)  
Figure 1.
Fig. 1. Architecture of the hydrophilic domain of T. thermophilus complex I. (A) Side view, with the membrane arm likely to be beneath and extending to the right, in the direction of helix H1. Each subunit is colored differently; FMN is shown as magenta spheres, metal sites as red spheres for Fe atoms and yellow spheres for S atoms. A possible quinone-binding site (Q) is indicated by an arrow. (B) Arrangement of redox centers. The overall orientation is similar to that in (A), tilted to provide an improved view of the FMN and the clusters. Cluster N1a is in subunit Nqo2; N3 and FMN in Nqo1; N1b, N4, N5, and N7 in Nqo3; N6a/b in Nqo9; and N2 in Nqo6. The main pathway of electron transfer is indicated by blue arrows, and a diversion to cluster N1a by a green arrow. The distances between the centers given in angstroms were calculated both center-to-center and edge-to-edge (shown in parentheses). Clusters N3 and N4 are separated by 17.6 Å (13.8 Å edge-to-edge), and clusters N1b and N5 by 19.2 Å (16.7 Å edge-to-edge).
Figure 2.
Fig. 2. The folds of individual subunits. Fe-S centers are shown as red spheres for Fe atoms and yellow spheres for S atoms, with cluster names in red. Subunits are not drawn to the same scale. (A) Nqo1. Its N-terminal domain is in purple, a Rossman-fold domain in blue, an ubiquitin-like domain in green, and the C-terminal helical bundle, coordinating cluster N3, in red. FMN is shown in stick representation. (B) Nqo2. The N-terminal helical bundle is shown in blue, the thioredoxin-like domain coordinating cluster N1a in green. (C) Nqo3. The N-terminal [FeFe]-hydrogenase-like domain coordinating clusters N1b, N4, and N5 is magenta, subdomains of the C-terminal molybdoenzyme-like domain are shown in I (coordinating cluster N7), blue; II, green; III, yellow; and IV, red. (D) Nqo9, coordinating clusters N6a and N6b, is shown in rainbow representation, colored blue to red from N to C terminus. (E) Nqo6, coordinating cluster N2, is shown in rainbow representation, with helix H1 indicated. (F) Nqo4. The N-terminal ß domain is shown in blue, the -helical bundle in green, the extended helix H2 in yellow, and the C-terminal ß domain in orange. Clusters are shown for orientation only. (G) Nqo5. The N-terminal /ß domain interacting with Nqo4 is shown in blue, the domain interacting with Nqo9 in green, and the C-terminal loop interacting with Nqo3 in yellow. Clusters are shown for orientation only. (H) Nqo15, shown in rainbow representation. The histidines exposed inside the putative iron storage cavity are shown.
  The above figures are reprinted by permission from the AAAs: Science (2006, 311, 1430-1436) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

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PDB code: 3rko
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PDB codes: 3m9c 3m9s
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PDB codes: 3i9v 3iam 3ias
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Shaping the mitochondrion: mitochondrial biogenesis, dynamics and dysfunction. Conference on Mitochondrial Assembly and Dynamics in Health and Disease.
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Dodecin is the key player in flavin homeostasis of archaea.
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PDB codes: 2vx9 2vxa
19672299 M.J.Falk, J.R.Rosenjack, E.Polyak, W.Suthammarak, Z.Chen, P.G.Morgan, and M.M.Sedensky (2009).
Subcomplex Ilambda specifically controls integrated mitochondrial functions in Caenorhabditis elegans.
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How mitochondria produce reactive oxygen species.
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Reduction of hydrophilic ubiquinones by the flavin in mitochondrial NADH:ubiquinone oxidoreductase (Complex I) and production of reactive oxygen species.
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Critical roles of subunit NuoH (ND1) in the assembly of peripheral subunits with the membrane domain of Escherichia coli NDH-1.
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19059197 R.Fato, C.Bergamini, M.Bortolus, A.L.Maniero, S.Leoni, T.Ohnishi, and G.Lenaz (2009).
Differential effects of mitochondrial Complex I inhibitors on production of reactive oxygen species.
  Biochim Biophys Acta, 1787, 384-392.  
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Analysis of CASP8 targets, predictions and assessment methods.
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19366614 V.Zickermann, S.Kerscher, K.Zwicker, M.A.Tocilescu, M.Radermacher, and U.Brandt (2009).
Architecture of complex I and its implications for electron transfer and proton pumping.
  Biochim Biophys Acta, 1787, 574-583.  
18502755 A.Galkin, B.Meyer, I.Wittig, M.Karas, H.Schägger, A.Vinogradov, and U.Brandt (2008).
Identification of the mitochondrial ND3 subunit as a structural component involved in the active/deactive enzyme transition of respiratory complex I.
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18757546 A.Miura, M.Kameya, H.Arai, M.Ishii, and Y.Igarashi (2008).
A soluble NADH-dependent fumarate reductase in the reductive tricarboxylic acid cycle of Hydrogenobacter thermophilus TK-6.
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18563446 C.Remacle, M.R.Barbieri, P.Cardol, and P.P.Hamel (2008).
Eukaryotic complex I: functional diversity and experimental systems to unravel the assembly process.
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18603533 E.Nakamaru-Ogiso, A.Matsuno-Yagi, S.Yoshikawa, T.Yagi, and T.Ohnishi (2008).
Iron-sulfur cluster N5 is coordinated by an HXXXCXXCXXXXXC motif in the NuoG subunit of Escherichia coli NADH:quinone oxidoreductase (complex I).
  J Biol Chem, 283, 25979-25987.  
18631365 E.Pierce, G.Xie, R.D.Barabote, E.Saunders, C.S.Han, J.C.Detter, P.Richardson, T.S.Brettin, A.Das, L.G.Ljungdahl, and S.W.Ragsdale (2008).
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum).
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A cytochrome c containing nitrate reductase plays a role in electron transport for denitrification in Thermus thermophilus without involvement of the bc respiratory complex.
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Protein co-evolution, co-adaptation and interactions.
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Iron-sulfur protein folds, iron-sulfur chemistry, and evolution.
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Mass spectrometry profiles superoxide-induced intramolecular disulfide in the FMN-binding subunit of mitochondrial Complex I.
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Regulation of oxidative phosphorylation, the mitochondrial membrane potential, and their role in human disease.
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Real-time electron transfer in respiratory complex I.
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Synthesis and characterization of new piperazine-type inhibitors for mitochondrial NADH-ubiquinone oxidoreductase (complex I).
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NADH oxidation drives respiratory Na+ transport in mitochondria from Yarrowia lipolytica.
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A perspective on Peter Mitchell and the chemiosmotic theory.
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Maturation of iron-sulfur proteins in eukaryotes: mechanisms, connected processes, and diseases.
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Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme.
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The crystal structure of Desulfovibrio vulgaris dissimilatory sulfite reductase bound to DsrC provides novel insights into the mechanism of sulfate respiration.
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PDB code: 2v4j
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Were there any "misassignments" among iron-sulfur clusters N4, N5 and N6b in NADH-quinone oxidoreductase (complex I)?
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Functional role of coenzyme Q in the energy coupling of NADH-CoQ oxidoreductase (Complex I): stabilization of the semiquinone state with the application of inside-positive membrane potential to proteoliposomes.
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Complex I within oxidatively stressed bovine heart mitochondria is glutathionylated on Cys-531 and Cys-704 of the 75-kDa subunit: potential role of CYS residues in decreasing oxidative damage.
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Reversible interconversion of carbon dioxide and formate by an electroactive enzyme.
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18982432 V.Zickermann, S.Dröse, M.A.Tocilescu, K.Zwicker, S.Kerscher, and U.Brandt (2008).
Challenges in elucidating structure and mechanism of proton pumping NADH:ubiquinone oxidoreductase (complex I).
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17583799 A.C.Gemperli, C.Schaffitzel, C.Jakob, and J.Steuber (2007).
Transport of Na(+) and K (+) by an antiporter-related subunit from the Escherichia coli NADH dehydrogenase I produced in Saccharomyces cerevisiae.
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17635416 A.J.Lambert, and M.D.Brand (2007).
Research on mitochondria and aging, 2006-2007.
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17854275 A.K.Doughan, and S.I.Dikalov (2007).
Mitochondrial redox cycling of mitoquinone leads to superoxide production and cellular apoptosis.
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17250770 A.M.Burroughs, S.Balaji, L.M.Iyer, and L.Aravind (2007).
A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.
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17605815 A.M.Burroughs, S.Balaji, L.M.Iyer, and L.Aravind (2007).
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
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17444656 C.L.Chen, L.Zhang, A.Yeh, C.A.Chen, K.B.Green-Church, J.L.Zweier, and Y.R.Chen (2007).
Site-specific S-glutathiolation of mitochondrial NADH ubiquinone reductase.
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17506638 D.C.Wallace (2007).
Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine.
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17640900 G.Yakovlev, T.Reda, and J.Hirst (2007).
Reevaluating the relationship between EPR spectra and enzyme structure for the iron sulfur clusters in NADH:quinone oxidoreductase.
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17436066 H.Sugiyama, R.Nakatsubo, S.Yamaguchi, T.Ogura, K.Shinzawa-Itoh, and S.Yoshikawa (2007).
Resonance Raman spectra of the FMN of the bovine heart NADH: ubiquinone oxidoreductase, the largest membrane protein in the mitochondrial respiratory system.
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18037377 I.S.Gostimskaya, V.G.Grivennikova, G.Cecchini, and A.D.Vinogradov (2007).
Reversible dissociation of flavin mononucleotide from the mammalian membrane-bound NADH: ubiquinone oxidoreductase (complex I).
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18240421 M.Hüttemann, I.Lee, L.Samavati, H.Yu, and J.W.Doan (2007).
Regulation of mitochondrial oxidative phosphorylation through cell signaling.
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17438127 M.Lazarou, M.McKenzie, A.Ohtake, D.R.Thorburn, and M.T.Ryan (2007).
Analysis of the assembly profiles for mitochondrial- and nuclear-DNA-encoded subunits into complex I.
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16969669 M.Long, J.Liu, Z.Chen, B.Bleijlevens, W.Roseboom, and S.P.Albracht (2007).
Characterization of a HoxEFUYH type of [NiFe] hydrogenase from Allochromatium vinosum and some EPR and IR properties of the hydrogenase module.
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18251921 N.Battchikova, and E.M.Aro (2007).
Cyanobacterial NDH-1 complexes: multiplicity in function and subunit composition.
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17557793 N.Buzhynskyy, P.Sens, V.Prima, J.N.Sturgis, and S.Scheuring (2007).
Rows of ATP synthase dimers in native mitochondrial inner membranes.
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17521330 P.Cermáková, Z.Verner, P.Man, J.Lukes, and A.Horváth (2007).
Characterization of the NADH:ubiquinone oxidoreductase (complex I) in the trypanosomatid Phytomonas serpens (Kinetoplastida).
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17591445 T.Clason, V.Zickermann, T.Ruiz, U.Brandt, and M.Radermacher (2007).
Direct localization of the 51 and 24 kDa subunits of mitochondrial complex I by three-dimensional difference imaging.
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Effects of the deletion of the Escherichia coli frataxin homologue CyaY on the respiratory NADH:ubiquinone oxidoreductase.
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17760425 V.G.Grivennikova, A.B.Kotlyar, J.S.Karliner, G.Cecchini, and A.D.Vinogradov (2007).
Redox-dependent change of nucleotide affinity to the active site of the mammalian complex I.
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16631892 C.Blakemore, and J.Davidson (2006).
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17010373 J.Chartron, K.S.Carroll, C.Shiau, H.Gao, J.A.Leary, C.R.Bertozzi, and C.D.Stout (2006).
Substrate recognition, protein dynamics, and iron-sulfur cluster in Pseudomonas aeruginosa adenosine 5'-phosphosulfate reductase.
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PDB code: 2goy
17050691 J.Zhang, F.E.Frerman, and J.J.Kim (2006).
Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.
  Proc Natl Acad Sci U S A, 103, 16212-16217.
PDB codes: 2gmh 2gmj
16911956 K.Z.Bencze, K.C.Kondapalli, J.D.Cook, S.McMahon, C.Millán-Pacheco, N.Pastor, and T.L.Stemmler (2006).
The structure and function of frataxin.
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16682634 L.Kussmaul, and J.Hirst (2006).
The mechanism of superoxide production by NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria.
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17092311 M.V.Busi, M.V.Maliandi, H.Valdez, M.Clemente, E.J.Zabaleta, A.Araya, and D.F.Gomez-Casati (2006).
Deficiency of Arabidopsis thaliana frataxin alters activity of mitochondrial Fe-S proteins and induces oxidative stress.
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16838076 R.J.Janssen, L.G.Nijtmans, L.P.van den Heuvel, and J.A.Smeitink (2006).
Mitochondrial complex I: structure, function and pathology.
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