TCDB is operated by the Saier Lab Bioinformatics Group
TCIDNameDomainKingdom/PhylumProtein(s)
*3.D.1.1.1









NADH dehydrogenase I, NuoA-N.  NuoL probably comprises part of the proton pathway (Nakamaru-Ogiso et al. 2010).  NuoL (ND5), NuoM (ND4) and NuoN (ND2) are all homologous to proton:sodium antiporters and may all play reoles in pumping protons using a similar mechanism (Sato et al. 2013).

Bacteria
Proteobacteria
NDH of E. coli NuoA-N
*3.D.1.2.1









NADH dehydrogenase I
Bacteria
Proteobacteria
NDH of Paracoccus denitrificans Nqo1-14
*3.D.1.3.1









NADH Dehydrogenase, NDH (Baradaran et al. 2013).  The x-ray structures of various complexes have been solved, and a coupling mechanism involving long range conformational changes has been proposed (Sazanov et al. 2013).

Bacteria
Deinococcus-Thermus
NDH of Thermus thermophilus HB-8 Nqo1-15
*3.D.1.4.1









Proton-translocating hydrogenase, H2ase
Archaea
Euryarchaeota
H2ase of Pyrococcus furiosus MbhA-N (PF1423-PF1436)
*3.D.1.4.2









[Ni2+-4Fe-4S] H+ translocating, quinone-independent ferredoxin:H+ oxidoreductase, EchA-F (Hedderich and Forzi, 2005; Künkel et al., 1998; Welte and Deppenmeier 2013) The Ech hydrogenases of M. mazei and M. barkeri have been characterized and were shown to pump protons (Welte et al., 2010).  The EchC and EcnF subunits include [Fe4S4] centers, and that in the EchC subunit exhibits a pH dependency to suggest that it plays a role in proton pumping (Forzi et al. 2005).  EchE has the NiFe center that converts 2H+ to H2.  The transmembrane subuits are EchA and EchB (Welte and Deppenmeier 2013) The Ech hydrogenases of M. mazei and M. barkeri have been characterized and were shown to pump protons (Welte et al., 2010).  The EchC and EcnF subunits include [Fe4S4] centers, and that in the EchC subunit exhibits a pH dependency to suggest that it plays a role in proton pumping (Forzi et al. 2005).  EchE has the NiFe center that converts 2H+ to H2.  The transmembrane subuits are EchA and EchB (Welte and Deppenmeier 2013).

Archaea
Euryarchaeota
EchABCDEF of Methanosarcina barkeri
EchA (639 aas; 16-18 TMSs; CAA76117)
EchB (285 aas; 7 TMSs; CAA76118)
EchC (156 aas; 0 TMSs; CAA76119)
EchD (113 aas; 0 or 1 TMSs; CAA76120)
EchE (358 aas; 4 TMSs; CAA76121)
EchF (122 aas; 0 TMSs; CAA76122)
*3.D.1.4.3









Carbon monoxide-induced, H+ translocating, quinone-independent, polyferredoxin (CooF):H+ oxidoreductase, H2ase (Fox et al., 1996a,b; Hedderich and Forzi, 2005) [oxidation of CO to CO2 by CO dehydrogenase results in transfer of electrons to polyferredoxin which reduces H2ase] (Soboh et al., 2002, 2004).

Bacteria
Proteobacteria
CooMKLXUH of Rhodospirillum rubrum
CooM (1265 aas; 32 TMSs; AAC45116)
CooK (323 aas; 7 TMSs; AAC45117)
CooL (142 aas; 4 TMSs; AAC45118)
CooX (166 aas; 4 TMSs; AAC45119)
CooU (172 aas; 0-4 TMSs; AAC45120)
CooH (361 aas; 2-4 TMSs; AAC45121)
*3.D.1.4.4









Energy conserving probable carbon monoxide-inducible hydrogenase, CooMKLXUH (Martins et al. 2016).

Bacteria
Proteobacteria
CooMKLXUH of Desulfovibrio vulgaris
*3.D.1.5.1









Proton-translocating NADH dehydrogenase I
Bacteria
Proteobacteria
NDH of Geobacter sulfurreducens
NuoA (142 aas) NP_954485
NuoB (170 aas) NP_951399
NuoC (162 aas) NP_951400
NuoD (390 aas) NP_951401
NuoE (173 aas) NP_951402
NuoF (591 aas) NP_951403
NuoG (677 aas) NP_954479
NuoH (329 aas) NP_954476
NuoI (176 aas) NP_954474
NuoJ (163 aas) NP_954473
NuoK (102 aas) NP_954472
NuoL (624 aas) NP_954471
NuoM (496 aas) NP_954470
NuoN (466 aas) NP_954469
*3.D.1.6.1









The vertebrate H+-translocating NADH dehydrogenase (NDH) complex (45 subunits) (Cardol et al., 2004).  The 3-d structure of the 44 subunit complex (14 core subunits present in bacteria, plus 30 additional subunits) with a molecular weight of 1 MDa, has been solved at 5 Å resolution by single particle electron cryo-microscopy (Vinothkumar et al. 2014).The core subunits contain eight iron-sulphur clusters and 60 transmembrane helices. The structures of many of the supernumerary subunits were determined or modeled. The structure provided insight into the roles of the supernumerary subunits in regulation, assembly and homeostasis.  One such subunit, GRIM-19 or NDUFA13, (Q9P0J0 of the human homologue) is essential for membrane potential formation and NADH assembly (Lu and Cao 2008).  Stroud et al. 2016 showed that 25 of the 31 accessory subunits in the 45 subunit human NADH dehydrogenase complex are required for assembly of a functional complex, and 1 subunit is essential for cell viability. Quantitative proteomic analysis revealed that loss of each subunit affects the stability of other subunits residing in the same structural module (Stroud et al. 2016). Leber's hereditary optic neuropathy (LHON) in humans is associated with combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I (Caporali et al. 2018).

Eukaryota
Metazoa
NDH of Bos taurus (45 subunits)
PSST (20) (NuoB) (P42026)
TYKY (23) (NuoI) (P42028)
24 (NuoE) (P04394)
30 (NuoC) (P23709)
49 (NuoD) (P17694)
51 (NuoF) (P25708)
75 (NuoG) (P15690)
ND1 (36) (NuoH) (P03887)
ND2 (39) (NuoN) (P03892)
ND3 (13) (NuoA) (P03898)
ND4 (52) (NuoM) (P03910)
ND4L (11) (NuoK) (P03902)
ND5 (67) (NuoL) (P03920)
ND6 (19) (NuoJ) (P03924)
MWFE (7.5) (Q02377)
SDAP (8) (P52505)
B8 (Q02370)
B12 (Q02365)
B13 (P23935)
13a (P23934)
B14 (Q02366)
ESSS (14.5) (Q8HXG5)
PFFD (15) (Q02379)
B16.6 (Q95KV7)
B17.2 (O97725)
B18 (Q02368)
AQDQ (18) (Q02375)
PGIV (19) (P42029)
B22 (Q02369)
PDSW (22) (Q9DCS9)
39 (P34943)
B14.7 (Q8HXG6)
B15 (P48305)
ASHI (19) (Q02372)
KFYI (6)6 (Q02376)
MNLL (7) (Q02378)
AGGG (8) (Q02374)
B95,6 (Q02371)
MLRQ (9) (Q01321)
106 (P25712)
B14.5a (Q05752)
B14.5b (Q02827)
SGDH (16) (Q02380)
B17 (Q02367)
42 (P34942)
*3.D.1.6.2









The fungal H+ translocating NADH dehydrogenase (NDH) complex (38 subunits; 35 included here) (Cardol et al., 2004).  The high resolution (3.6 - 3.9 Å) structure of the mitochondrial Yarrowia lipolytica enzyme, showing all central subunits that execute the bioenergetic functions, has been solved (see discussion for TC# 3.A.1 and Zickermann et al. 2015).

Eukaryota
Fungi
NDH of Neurospora crassa (35 subunits):
19.3 (NuoB) (O47950)
21.3c (NuoI) (Q12644)
24 (NuoE) (P40915)
31 (NuoC) (P23710)
49 (NuoD) (P22142)
51 (NuoF) (P24917)
78 (NuoG) (P24918)
ND1 (42) (NuoH) (P08774)
ND2 (66) (NuoN) (Q35140)
ND3 (NuoA) (Q35141)
ND4 (NuoM) (P15582)
ND4L (10) (NuoK) (P05509)
ND5 (80) (NuoL) (P05510)
ND6 (NuoJ) (P15959)
9.8 (Q6MFL8)
9.6 (P11943)
10.5 (Q07842)
10.63 (XP_331394)
29.9 (P24919)
18.43(Q7RWU3)
14.8 (P42114)
11.73 (XP_324110)
11.53 (Q9P6T9)
13.53 (P7S1I2)
13.43 (Q8X0V6)
89.73 (Q7RZ09)
21 (P25711)
20.8 (P21976)
183 (Q875B9)
12.3 (Q03015)
40 (P25284)
21.3B (P25710)
73 (XP_322246)
20.13 (XP_332152)
20.9 (Q02854)
*3.D.1.6.3









The higher plant H+ translocating NADH dehydrogenase (NDH) complex (41 subunits; 23 included here) (Cardol et al., 2004)
Eukaryota
Viridiplantae
NDH of Arabidopsis thaliana (32 subunits)
24 (NuoB) (Q42577)
25.5 (NuoI) (Q9FX83)
28.3 (NuoE) (O22769)
ND9 (22.6) (NuoC) (Q95748)
ND7 (44.6) (NuoD) (P93306)
53.5 (NuoF) (Q9FNN5)
81.5 (NuoG) (Q9FGI6)
ND1 (36) (NuoH) (NP_085565)
ND2 (55) (NuoN) (NP_085584)
ND3 (14) (NuoA) (NP_085553)
ND4 (55) (NuoM) (NP_085518)
ND4L (11) (NuoK) (NP_051111)
ND5 (74) (NuoL) (NP_085478)
ND6 (23.5) (NuoJ) (NP_085495)
7.5 (Q84MD9)
14 (O80800)
10.8 (Q8FIJ2)
7 (AK059007)
19.2 (Q9FLX7)
12.2 (Q9M9M6)
15 (Q9LHI0)
133 (Q8L3S7)
14 (Q9LZI6)
16.1 (Q8RWA7)
18 (Q9M9M9)
12 (Q8GXZ6)
17.1 (Q9FJW4)
12 (Q8LGE7)
13.6 (Q945M1)
12.5 (Q84W12)
44 (Q9SK66)
*3.D.1.6.4









The green algal H+ translocating NADH dehydrogenase (NDH) complex (42 subunits; 33 included here) (Cardol et al., 2004)
Eukaryota
Viridiplantae
NDH of Chlamydomonas reinhardtii (33 subunits)
18 (NuoB) (Q6V9B0)
23 (NuoI) (Q6V9B1)
27 (NuoE) (Q6V9B3)
25 (NuoC) (Q6V5O7)
43 (NuoD) (Q6V9A8)
50 (NuoF) (Q6V9B2)
75 (NuoG) (Q6UKY6)
ND1 (31.6) (NuoH) (P11658)
ND2 (42.4) (NuoN) (P08740)
14 (NuoA) (Q6V502)
ND4 (48.7) (NuoM) (P20113)
24.2 (NuoK) (Q84K56)
ND5 (59) (NuoL) (P08739)
ND6 (17.7) (NuoJ) (P10329)
7.53 (Q6Q1V4)
143 (Q6UKY4)
11 (Q6V9A9)
6.53 (Q6Q1V8)
18 (Q6UKY3)
133 (Q6UP30)
14 (Q6UKY9)
17 (Q6Q1W0)
11 (Q6TH88)
16 (Q6UP32)
18 (Q6UP31)
12 (Q6UKY7)
19 (Q6UP29)
12.93 (Q6V504)
13.93 (Q6UKY8)
17 (Q6V505)
38 (Q6V506)
23 (Q6QAY4)
13 (Q9UP28)
*3.D.1.7.1









The NADH: ubiquinone oxidoreductase homologue using flavodoxin rather than NADH as electron donor (Weerakoon and Olson, 2008),
Bacteria
Proteobacteria
Flavodoxin: ubiquinone oxidoreductase of Campylobacter jejuni
NuoA Q0P849
NuoB Q0P850
NuoC Q0P851
NuoD Q9PM99
NuoG Q0P855
NuoH Q9PMA3
NuoI Q0P857
NuoJ Q0P858
NuoK Q0P859
NuoL Q9PMA7
NuoM Q0P861
NuoN Q0P862
Cj1575c (NuoE) Q0P853
Cj1574c (NuoF) Q0P854
*3.D.1.8.1









The chloroplast NDH-1 complex with form subcomplexes, subcomplex: M (membrane). L (lumen), A and B (Peng et al., 2011).  The NDF6 (PNSB6) protein is essential for activity (Ishikawa et al. 2008).

Eukaryota
Viridiplantae
NDH complex of Arabidopsis thaliana chloroplasts
NdhA (Q37165) = NuoH in E. coli
NdhB (P0CC32) = NuoN in E. coli
NdhC (P56751) = NuoA in E. coli
NdhD (P26288) = NuoM in E. coli
NdhE (P26289) = NuoK in E. coli
NdhF (P56752) = NuoL in E. coli
NdhG (Q95695) = NuoJ in E. coli
NdhH (P56753) = NuoD in E. coli
NdhI (P56755) = NuoI in E. coli
NdhJ (P56754) =  NuoC in E. coli
NdhK (P56756) = NuoB in E. coli
NdhL (Q9CAC5)
NdhM (Q2V2S7)
NdhN (B3H5R4)
NdhO (Q9S829)
NDF1 (Q9S9N6)
NDF2 (C0Z2H4)
NDF4 (Q9LU21)
NDF6 (B3H6Z4)
NDH18 (Q9FG89)
PQL (Q9SGH4)
PPL2 (O80634)
CYP20-2 (F4K2G0)
FKBP16-2 (F4JW56)
PQL (Q9XI73)   
*3.D.1.9.1









Hydrogenase 4, Hyf. Catalyzes H2 production and H+/K+ exchange (Bagramyan et al., 2001; 2002).

Bacteria
Proteobacteria
Hydrogenase 4 (HyfABCDEFGHI) of E. coli
HyfA (P23481)
HyfB (P23482)
HyfC (P77858)
HyfD (P77416)
HyfE (P0AEW1)
HyfF (P77437)
HyfG (P77329)
HyfH (P77423)
HyfI (P77668)
*3.D.1.9.2









Hydrogenase 3, Hyc. Catalyzes H2 production coupled to H+ export (Bagramyan et al., 2002). The HycC and HycD proteins span the membrane multiple times; FdhF is a molybdenum-dependent formate dehydrogenase while HycE (Hyd-3) is a NiFe hydrogenase (McDowall et al. 2014).

Bacteria
Proteobacteria
Hydrogenase 3, HycBCDEF of E. coli 
HycB (like HyfA) (P0AAK3)
HycC (like HyfB) (P16429) 
HycD (like HyfC) (P16430)
HycE (like HyfD) (P16431)
HycF (like HyfE) (P16432)
HycG (like HyfF) (P16433)
FdhF (FHL) (P07658)
*3.D.1.9.3









Putative hydrogenase 4, HyfA-I. 

Bacteria
Spirochaetes
HyfA-I (H missing) of Leptospira interrogans 
HyfA (99aas) (Q8EXV0)
HyfB (573aas) (Q8EYE3)
HyfC (295aas) (Q8EYE2)
HyfD (519aas) (Q8F7D6)
HyfE (206aas) (Q8EYE1)
HyfF (402aas) (Q8EYD0)
HyfG (466aas) (Q8EYD9)
HyfI (273aas) (Q8EYD8)