respiratory complex i respiratory complex i respiratory complex i, ec 7.1.1.2 (also known as nadh:ubiquinone oxidoreductase, type i nadh dehydrogenase and mitochondrial complex i) is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. it catalyzes the transfer of electrons from nadh to coenzyme q10 (coq10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria. respiratory complex iidentifierssymbolrespiratory complex iopm superfamily246opm protein6g72membranome255 nadh:ubiquinone reductase (h+-translocating).identifiersec no.1.6.5.3databasesintenzintenz viewbrendabrenda entryexpasynicezyme viewkeggkegg entrymetacycmetabolic pathwaypriamprofilepdb structuresrcsb pdb pdbe pdbsumgene ontologyamigo / quickgosearchpmcarticlespubmedarticlesncbiproteins nadh dehydrogenase mechanism: 1. the seven primary iron sulfur centers serve to carry electrons from the site of nadh dehydration to ubiquinone. note that n7 is not found in eukaryotes. 2. there is a reduction of ubiquinone (coq) to ubiquinol (coqh2). 3. the energy from the redox reaction results in conformational change allowing hydrogen ions to pass through four transmembrane helix channels. this enzyme is essential for the normal functioning of cells, and mutations in its subunits lead to a wide range of inherited neuromuscular and metabolic disorders. defects in this enzyme are responsible for the development of several pathological processes such as ischemia/reperfusion damage (stroke and cardiac infarction), parkinson's disease and others. function nad+ to nadh. fmn to fmnh2. coq to coqh2. complex i is the first enzyme of the mitochondrial electron transport chain. there are three energy-transducing enzymes in the electron transport chain - nadh:ubiquinone oxidoreductase (complex i), coenzyme q – cytochrome c reductase (complex iii), and cytochrome c oxidase (complex iv). complex i is the largest and most complicated enzyme of the electron transport chain. the reaction catalyzed by complex i is: nadh + h+ + coq + 4h+in→ nad+ + coqh2 + 4h+out in this process, the complex translocates four protons across the inner membrane per molecule of oxidized nadh, helping to build the electrochemical potential difference used to produce atp. escherichia coli complex i (nadh dehydrogenase) is capable of proton translocation in the same direction to the established δψ, showing that in the tested conditions, the coupling ion is h+. na+ transport in the opposite direction was observed, and although na+ was not necessary for the catalytic or proton transport activities, its presence increased the latter. h+ was translocated by the paracoccus denitrificans complex i, but in this case, h+ transport was not influenced by na+, and na+ transport was not observed. possibly, the e. coli complex i has two energy coupling sites (one na+ independent and the other na+dependent), as observed for the rhodothermus marinus complex i, whereas the coupling mechanism of the p. denitrificans enzyme is completely na+ independent. it is also possible that another transporter catalyzes the uptake of na+. complex i energy transduction by proton pumping may not be exclusive to the r. marinus enzyme. the na+/h+ antiport activity seems not to be a general property of complex i. however, the existence of na+-translocating activity of the complex i is still in question. the reaction can be reversed – referred to as aerobic succinate-supported nad+ reduction by ubiquinol – in the presence of a high membrane potential, but the exact catalytic mechanism remains unknown. driving force of this reaction is a potential across the membrane which can be maintained either by atp-hydrolysis or by complexes iii and iv during succinate oxidation. complex i may have a role in triggering apoptosis. in fact, there has been shown to be a correlation between mitochondrial activities and programmed cell death (pcd) during somatic embryo development. complex i is not homologous to na+-translocating nadh dehydrogenase (ndh) family (tc# 3.d.1), a member of the na+ transporting mrp superfamily. as a result of a two nadh molecule being oxidized to nad+, three molecules of atp can be produced by complex v (atp synthase) downstream in the respiratory chain. mechanism overall mechanism all redox reactions take place in the hydrophilic domain of complex i. nadh initially binds to complex i, and transfers two electrons to the flavin mononucleotide (fmn) prosthetic group of the enzyme, creating fmnh2. the electron acceptor – the isoalloxazine ring – of fmn is identical to that of fad. the electrons are then transferred through the fmn via a series of iron-sulfur (fe-s) clusters, and finally to coenzyme q10 (ubiquinone). this electron flow changes the redox state of the protein, inducing conformational changes of the protein which alters the pk values of ionizable side chain, and causes four hydrogen ions to be pumped out of the mitochondrial matrix. ubiquinone (coq) accepts two electrons to be reduced to ubiquinol (coqh2). electron transfer mechanism the proposed pathway for electron transport prior to ubiquinone reduction is as follows: nadh – fmn – n3 – n1b – n4 – n5 – n6a – n6b – n2 – q, where nx is a labelling convention for iron sulfur clusters. the high reduction potential of the n2 cluster and the relative proximity of the other clusters in the chain enable efficient electron transfer over long distance in the protein (with transfer rates from nadh to n2 iron-sulfur cluster of about 100 μs). the equilibrium dynamics of complex i are primarily driven by the quinone redox cycle. in conditions of high proton motive force (and accordingly, a ubiquinol-concentrated pool), the enzyme runs in the reverse direction. ubiquinol is oxidized to ubiquinone, and the resulting released protons reduce the proton motive force. proton translocation mechanism the coupling of proton translocation and electron transport in complex i is currently proposed as being indirect (long range conformational changes) as opposed to direct (redox intermediates in the hydrogen pumps as in heme groups of complexes iii and iv). the architecture of the hydrophobic region of complex i shows multiple proton transporters that are mechanically interlinked. the three central components believed to contribute to this long-range conformational change event are the ph-coupled n2 iron-sulfur cluster, the quinone reduction, and the transmembrane helix subunits of the membrane arm. transduction of conformational changes to drive the transmembrane transporters linked by a 'connecting rod' during the reduction of ubiquinone can account for two or three of the four protons pumped per nadh oxidized. the remaining proton must be pumped by direct coupling at the ubiquinone-binding site. it is proposed that direct and indirect coupling mechanisms account for the pumping of the four protons. the n2 cluster's proximity to a nearby cysteine residue results in a conformational change upon reduction in the nearby helices, leading to small but important changes in the overall protein conformation. further electron paramagnetic resonance studies of the electron transfer have demonstrated that most of the energy that is released during the subsequent coq reduction is on the final ubiquinol formation step from semiquinone, providing evidence for the "single stroke" h+ translocation mechanism (i.e. all four protons move across the membrane at the same time). alternative theories suggest a "two stroke mechanism" where each reduction step (semiquinone and ubiquinol) results in a stroke of two protons entering the intermembrane space. the resulting ubiquinol localized to the membrane domain interacts with negatively charged residues in the membrane arm, stabilizing conformational changes. an antiporter mechanism (na+/h+ swap) has been proposed using evidence of conserved asp residues in the membrane arm. the presence of lys, glu, and his residues enable for proton gating (a protonation followed by deprotonation event across the membrane) driven by the pka of the residues. composition and structure nadh:ubiquinone oxidoreductase is the largest of the respiratory complexes. in mammals, the enzyme contains 44 separate water-soluble peripheral membrane proteins, which are anchored to the integral membrane constituents. of particular functional importance are the flavin prosthetic group (fmn) and eight iron-sulfur clusters (fes). of the 44 subunits, seven are encoded by the mitochondrial genome. the structure is an "l" shape with a long membrane domain (with around 60 trans-membrane helices) and a hydrophilic (or peripheral) domain, which includes all the known redox centres and the nadh binding site. all thirteen of the e. coli proteins, which comprise nadh dehydrogenase i, are encoded within the nuo operon, and are homologous to mitochondrial complex i subunits. the antiporter-like subunits nuol/m/n each contains 14 conserved transmembrane (tm) helices. two of them are discontinuous, but subunit nuol contains a 110 å long amphipathic α-helix, spanning the entire length of the domain. the subunit, nuol, is related to na+/ h+ antiporters of tc# 2.a.63.1.1 (phaa and phad). three of the conserved, membrane-bound subunits in nadh dehydrogenase are related to each other, and to mrp sodium-proton antiporters. structural analysis of two prokaryotic complexes i revealed that the three subunits each contain fourteen transmembrane helices that overlay in structural alignments: the translocation of three protons may be coordinated by a lateral helix connecting them. complex i contains a ubiquinone binding pocket at the interface of the 49-kda and psst subunits. close to iron-sulfur cluster n2, the proposed immediate electron donor for ubiquinone, a highly conserved tyrosine constitutes a critical element of the quinone reduction site. a possible quinone exchange path leads from cluster n2 to the n-terminal beta-sheet of the 49-kda subunit. all 45 subunits of the bovine ndhi have been sequenced. each complex contains noncovalently bound fmn, coenzyme q and several iron-sulfur centers. the bacterial ndhs have 8-9 iron-sulfur centers. a recent study used electron paramagnetic resonance (epr) spectra and double electron-electron resonance (deer) to determine the path of electron transfer through the iron-sulfur complexes, which are located in the hydrophilic domain. seven of these clusters form a chain from the flavin to the quinone binding sites; the eighth cluster is located on the other side of the flavin, and its function is unknown. the epr and deer results suggest an alternating or “roller-coaster” potential energy profile for the electron transfer between the active sites and along the iron-sulfur clusters, which can optimize the rate of electron travel and allow efficient energy conversion in complex i. conserved subunits of complex i # human/bovine subunit human protein protein description (uniprot) pfam family with human protein core subunitsa 1ndufs7 / psst / nukmndus7_humannadh dehydrogenase iron-sulfur protein 7, mitochondrial ec 1.6.5.3 ec 1.6.99.3pfam pf01058 2ndufs8 / tyky / nuimndus8_humannadh dehydrogenase iron-sulfur protein 8, mitochondrial ec 1.6.5.3 ec 1.6.99.3pfam pf12838 3ndufv2 / 24kd / nuhmcnduv2_humannadh dehydrogenase flavoprotein 2, mitochondrial ec 1.6.5.3 ec 1.6.99.3pfam pf01257 4ndufs3 / 30kd / nugmndus3_humannadh dehydrogenase iron-sulfur protein 3, mitochondrial ec 1.6.5.3 ec 1.6.99.3pfam pf00329 5ndufs2 / 49kd / nucmndus2_humannadh dehydrogenase iron-sulfur protein 2, mitochondrial ec 1.6.5.3 ec 1.6.99.3pfam pf00346 6ndufv1 / 51kd / nubmnduv1_humannadh dehydrogenase flavoprotein 1, mitochondrial ec 1.6.5.3 ec 1.6.99.3pfam pf01512 7ndufs1 / 75kd / nuamndus1_humannadh-ubiquinone oxidoreductase 75 kda subunit, mitochondrial ec 1.6.5.3 ec 1.6.99.3pfam pf00384 8nd1 / nu1mnu1m_humannadh-ubiquinone oxidoreductase chain 1 ec 1.6.5.3pfam pf00146 9nd2 / nu2mnu2m_humannadh-ubiquinone oxidoreductase chain 2 ec 1.6.5.3pfam pf00361, pfam pf06444 10nd3 / nu3mnu3m_humannadh-ubiquinone oxidoreductase chain 3 ec 1.6.5.3pfam pf00507 11nd4 / nu4mnu4m_humannadh-ubiquinone oxidoreductase chain 4 ec 1.6.5.3pfam pf01059, pfam pf00361 12nd4l / nulmnu4lm_humannadh-ubiquinone oxidoreductase chain 4l ec 1.6.5.3pfam pf00420 13nd5 / nu5mnu5m_humannadh-ubiquinone oxidoreductase chain 5 ec 1.6.5.3pfam pf00361, pfam pf06455, pfam pf00662 14nd6 / nu6mnu6m_humannadh-ubiquinone oxidoreductase chain 6 ec 1.6.5.3pfam pf00499 core accessory subunitsb 15ndufs6 / 13andus6_humannadh dehydrogenase iron-sulfur protein 6, mitochondrialpfam pf10276 16ndufa12 / b17.2nduac_humannadh dehydrogenase 1 alpha subcomplex subunit 12pfam pf05071 17ndufs4 / aqdqndus4_humannadh dehydrogenase iron-sulfur protein 4, mitochondrialpfam pf04800 18ndufa9 / 39kdandua9_humannadh dehydrogenase 1 alpha subcomplex subunit 9, mitochondrialpfam pf01370 19ndufab1 / acpmacpm_humanacyl carrier protein, mitochondrialpfam pf00550 20ndufa2 / b8ndua2_humannadh dehydrogenase 1 alpha subcomplex subunit 2pfam pf05047 21ndufa1 / mfwendua1_humannadh dehydrogenase 1 alpha subcomplex subunit 1pfam pf15879 22ndufb3 / b12ndub3_humannadh dehydrogenase 1 beta subcomplex subunit 3pfam pf08122 23ndufa5 / ab13ndua5_humannadh dehydrogenase 1 alpha subcomplex subunit 5pfam pf04716 24ndufa6 / b14ndua6_humannadh dehydrogenase 1 alpha subcomplex subunit 6pfam pf05347 25ndufa11 / b14.7nduab_humannadh dehydrogenase 1 alpha subcomplex subunit 11pfam pf02466 26ndufb11 / esssndubb_humannadh dehydrogenase 1 beta subcomplex subunit 11, mitochondrialpfam pf10183 27ndufs5 / pffdndus5_humannadh dehydrogenase iron-sulfur protein 5pfam pf10200 28ndufb4 / b15ndub4_humannadh dehydrogenase 1 beta subcomplex subunit 4pfam pf07225 29ndufa13 /a13nduad_humannadh dehydrogenase 1 alpha subcomplex subunit 13pfam pf06212 30ndufb7 / b18ndub7_humannadh dehydrogenase 1 beta subcomplex subunit 7pfam pf05676 31ndufa8 / pgivndua8_humannadh dehydrogenase 1 alpha subcomplex subunit 8pfam pf06747 32ndufb9 / b22ndub9_humannadh dehydrogenase 1 beta subcomplex subunit 9pfam pf05347 33ndufb10 / pdswnduba_humannadh dehydrogenase 1 beta subcomplex subunit 10pfam pf10249 34ndufb8 / ashindub8_humannadh dehydrogenase 1 beta subcomplex subunit 8, mitochondrialpfam pf05821 35ndufc2 / b14.5bnduc2_humannadh dehydrogenase 1 subunit c2pfam pf06374 36ndufb2 / agggndub2_humannadh dehydrogenase 1 beta subcomplex subunit 2, mitochondrialpfam pf14813 37ndufa7 / b14.5andua7_humannadh