Summary

FAD/NAD(P)-binding Rossmann fold Superfamily

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

This clan contains 209 families and the total number of domains in the clan is 2755088. The clan was built by RD Finn.

Literature references

Bashton M, Chothia C; , J Mol Biol 2002;315:927-939.: The geometry of domain combination in proteins. PUBMED:11812158 EPMC:11812158

Members

This clan contains the following 209 member families:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 BMT5-like BpsA_C CARME CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF268 DUF2855 DUF3410 DUF364 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C KR LCM Ldh_1_N LpxI_N Lycopene_cycl Lys_Orn_oxgnase Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MmeI_Mtase MOLO1 Mqo MT-A70 MTS Mur_ligase N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall OpcA_G6PD_assem Orbi_VP4 PALP PARP_regulatory PCMT PDH_N PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth SRR1 TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N

External database links

CATH:	3.40.50.720 3.40.50.1320
SCOP:	51984 51904 51971 51734

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

Loading domain graphics...

Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family	Num. domains	Alignment
adh_short (PF00106)	202553 (7.4%)	View
adh_short_C2 (PF13561)	181249 (6.6%)	View
Pyr_redox_2 (PF07992)	146063 (5.3%)	View
ADH_zinc_N (PF00107)	119198 (4.3%)	View
Epimerase (PF01370)	84450 (3.1%)	View
FAD_binding_3 (PF01494)	77886 (2.8%)	View
DAO (PF01266)	73495 (2.7%)	View
PALP (PF00291)	73067 (2.7%)	View
GFO_IDH_MocA (PF01408)	66899 (2.4%)	View
Methyltransf_11 (PF08241)	66412 (2.4%)	View
Methyltransf_25 (PF13649)	57976 (2.1%)	View
2-Hacid_dh_C (PF02826)	52138 (1.9%)	View
Amino_oxidase (PF01593)	47432 (1.7%)	View
Methyltransf_23 (PF13489)	38627 (1.4%)	View
GMC_oxred_N (PF00732)	36991 (1.3%)	View
ThiF (PF00899)	36637 (1.3%)	View
NAD_binding_10 (PF13460)	36336 (1.3%)	View
GDP_Man_Dehyd (PF16363)	34287 (1.2%)	View
NAD_binding_2 (PF03446)	34118 (1.2%)	View
FAD_binding_2 (PF00890)	33701 (1.2%)	View
FMO-like (PF00743)	33357 (1.2%)	View
NAD_binding_8 (PF13450)	29040 (1.1%)	View
TrkA_N (PF02254)	28982 (1.1%)	View
3HCDH_N (PF02737)	27558 (1.0%)	View
Mur_ligase (PF01225)	25259 (0.9%)	View
ADH_zinc_N_2 (PF13602)	24352 (0.9%)	View
B12-binding (PF02310)	23984 (0.9%)	View
MTS (PF05175)	23633 (0.9%)	View
NmrA (PF05368)	22779 (0.8%)	View
KR (PF08659)	22390 (0.8%)	View
Methyltr_RsmB-F (PF01189)	20653 (0.7%)	View
DNA_methylase (PF00145)	20330 (0.7%)	View
Semialdhyde_dh (PF01118)	20325 (0.7%)	View
F420_oxidored (PF03807)	20114 (0.7%)	View
UDPG_MGDP_dh_N (PF03721)	18854 (0.7%)	View
Ldh_1_N (PF00056)	18809 (0.7%)	View
Gp_dh_N (PF00044)	18775 (0.7%)	View
Methyltransf_31 (PF13847)	18387 (0.7%)	View
Methyltransf_2 (PF00891)	17897 (0.6%)	View
FtsJ (PF01728)	17089 (0.6%)	View
Malic_M (PF03949)	16917 (0.6%)	View
ELFV_dehydrog (PF00208)	16916 (0.6%)	View
NAD_binding_4 (PF07993)	16645 (0.6%)	View
Methyltransf_16 (PF10294)	15409 (0.6%)	View
CoA_binding (PF02629)	14842 (0.5%)	View
N6_Mtase (PF02384)	14539 (0.5%)	View
THF_DHG_CYH_C (PF02882)	14454 (0.5%)	View
PrmA (PF06325)	14115 (0.5%)	View
AlaDh_PNT_C (PF01262)	13512 (0.5%)	View
RrnaAD (PF00398)	13367 (0.5%)	View
PCMT (PF01135)	13318 (0.5%)	View
N6_N4_Mtase (PF01555)	13066 (0.5%)	View
Shikimate_DH (PF01488)	12923 (0.5%)	View
tRNA_U5-meth_tr (PF05958)	12566 (0.5%)	View
NAD_Gly3P_dh_N (PF01210)	12546 (0.5%)	View
Sacchrp_dh_NADP (PF03435)	12337 (0.4%)	View
NAD_binding_3 (PF03447)	11861 (0.4%)	View
GIDA (PF01134)	11840 (0.4%)	View
CMAS (PF02353)	11696 (0.4%)	View
CoA_binding_2 (PF13380)	11508 (0.4%)	View
Methyltransf_3 (PF01596)	11359 (0.4%)	View
ApbA (PF02558)	11330 (0.4%)	View
G6PD_N (PF00479)	11139 (0.4%)	View
Spermine_synth (PF01564)	11054 (0.4%)	View
RmlD_sub_bind (PF04321)	11034 (0.4%)	View
DFP (PF04127)	10363 (0.4%)	View
AdoHcyase_NAD (PF00670)	10287 (0.4%)	View
Methyltransf_4 (PF02390)	10277 (0.4%)	View
DapB_N (PF01113)	10244 (0.4%)	View
GRAS (PF03514)	10134 (0.4%)	View
Ubie_methyltran (PF01209)	9972 (0.4%)	View
YjeF_N (PF03853)	9869 (0.4%)	View
Methyltransf_12 (PF08242)	9812 (0.4%)	View
CheR (PF01739)	9610 (0.3%)	View
Methyltransf_5 (PF01795)	9400 (0.3%)	View
Methyltransf_21 (PF05050)	9203 (0.3%)	View
CoA_binding_3 (PF13727)	8950 (0.3%)	View
IlvN (PF07991)	8870 (0.3%)	View
Cons_hypoth95 (PF03602)	8635 (0.3%)	View
UPF0020 (PF01170)	8573 (0.3%)	View
HI0933_like (PF03486)	8517 (0.3%)	View
FAD_oxidored (PF12831)	8239 (0.3%)	View
GidB (PF02527)	8136 (0.3%)	View
OCD_Mu_crystall (PF02423)	8052 (0.3%)	View
PDH_N (PF02153)	7752 (0.3%)	View
Methyltransf_29 (PF03141)	7545 (0.3%)	View
3Beta_HSD (PF01073)	7490 (0.3%)	View
LCM (PF04072)	7433 (0.3%)	View
DXP_reductoisom (PF02670)	7433 (0.3%)	View
Polysacc_synt_2 (PF02719)	7248 (0.3%)	View
Methyltrans_SAM (PF10672)	7229 (0.3%)	View
XdhC_C (PF13478)	7184 (0.3%)	View
DXPR_C (PF13288)	7118 (0.3%)	View
NAD_binding_7 (PF13241)	6742 (0.2%)	View
TPM_phosphatase (PF04536)	6670 (0.2%)	View
GDI (PF00996)	6551 (0.2%)	View
Methyltransf_28 (PF02636)	6238 (0.2%)	View
Methyltransf_24 (PF13578)	6172 (0.2%)	View
Mannitol_dh (PF01232)	6147 (0.2%)	View
Methyltransf_19 (PF04672)	5791 (0.2%)	View
Trp_halogenase (PF04820)	5052 (0.2%)	View
Methyltransf_7 (PF03492)	4896 (0.2%)	View
MethyltransfD12 (PF02086)	4797 (0.2%)	View
Urocanase (PF01175)	4769 (0.2%)	View
Methyltransf_32 (PF13679)	4699 (0.2%)	View
continued

Pfam family	Num. domains	Alignment
MT-A70 (PF05063)	4629 (0.2%)	View
Glyco_tran_WecG (PF03808)	4423 (0.2%)	View
TRM (PF02005)	4391 (0.2%)	View
Methyltr_RsmF_N (PF17125)	4384 (0.2%)	View
GCD14 (PF08704)	4351 (0.2%)	View
Lys_Orn_oxgnase (PF13434)	4157 (0.2%)	View
Glyco_hydro_4 (PF02056)	4041 (0.1%)	View
Methyltransf_33 (PF10017)	4024 (0.1%)	View
Met_10 (PF02475)	4014 (0.1%)	View
Bac_GDH (PF05088)	3586 (0.1%)	View
TPMT (PF05724)	3500 (0.1%)	View
NAD_binding_9 (PF13454)	3405 (0.1%)	View
Rsm22 (PF09243)	3247 (0.1%)	View
Methyltransf_10 (PF05971)	3084 (0.1%)	View
CbiJ (PF02571)	3026 (0.1%)	View
NAD_binding_5 (PF07994)	3003 (0.1%)	View
Methyltransf_30 (PF05430)	2752 (0.1%)	View
Pox_MCEL (PF03291)	2736 (0.1%)	View
MmeI_Mtase (PF20473)	2704 (0.1%)	View
GLF (PF03275)	2614 (0.1%)	View
Methyltransf_15 (PF09445)	2586 (0.1%)	View
DOT1 (PF08123)	2571 (0.1%)	View
PglD_N (PF17836)	2543 (0.1%)	View
Fibrillarin (PF01269)	2527 (0.1%)	View
SE (PF08491)	2503 (0.1%)	View
Lycopene_cycl (PF05834)	2487 (0.1%)	View
CARME (PF07942)	2413 (0.1%)	View
BMT5-like (PF10354)	2403 (0.1%)	View
Methyltransf_PK (PF05891)	2353 (0.1%)	View
Mqo (PF06039)	2294 (0.1%)	View
RsmJ (PF04378)	2230 (0.1%)	View
SRR1 (PF07985)	2195 (0.1%)	View
Rossmann-like (PF10727)	2180 (0.1%)	View
DUF938 (PF06080)	2150 (0.1%)	View
PRMT5 (PF05185)	2133 (0.1%)	View
N6-adenineMlase (PF10237)	1933 (0.1%)	View
Eco57I (PF07669)	1898 (0.1%)	View
Methyltransf_8 (PF05148)	1886 (0.1%)	View
Prenylcys_lyase (PF07156)	1880 (0.1%)	View
OpcA_G6PD_assem (PF10128)	1810 (0.1%)	View
MetW (PF07021)	1778 (0.1%)	View
Methyltransf_14 (PF08484)	1685 (0.1%)	View
SAM_MT (PF04445)	1646 (0.1%)	View
Bin3 (PF06859)	1637 (0.1%)	View
rRNA_methylase (PF06962)	1539 (0.1%)	View
MCRA (PF06100)	1505 (0.1%)	View
AdoMet_MTase (PF07757)	1425 (0.1%)	View
DUF1611_N (PF17396)	1357 (0.0%)	View
LpxI_N (PF17930)	1351 (0.0%)	View
TylF (PF05711)	1316 (0.0%)	View
TRM13 (PF05206)	1272 (0.0%)	View
Methyltransf_9 (PF08003)	1220 (0.0%)	View
Methyltransf_22 (PF13383)	1206 (0.0%)	View
NNMT_PNMT_TEMT (PF01234)	1156 (0.0%)	View
Enoyl_reductase (PF12241)	1139 (0.0%)	View
Eno-Rase_FAD_bd (PF07055)	1121 (0.0%)	View
Eno-Rase_NADH_b (PF12242)	1112 (0.0%)	View
Bmt2 (PF11968)	1069 (0.0%)	View
NAS (PF03059)	1047 (0.0%)	View
TrmK (PF04816)	1000 (0.0%)	View
DUF1442 (PF07279)	978 (0.0%)	View
Methyltransf_18 (PF12847)	885 (0.0%)	View
DUF364 (PF04016)	849 (0.0%)	View
Polysacc_syn_2C (PF08485)	844 (0.0%)	View
Glu_dehyd_C (PF16912)	820 (0.0%)	View
NodS (PF05401)	781 (0.0%)	View
DREV (PF05219)	770 (0.0%)	View
TehB (PF03848)	752 (0.0%)	View
DUF3410 (PF11890)	723 (0.0%)	View
Mg-por_mtran_C (PF07109)	718 (0.0%)	View
DUF2855 (PF11017)	689 (0.0%)	View
Methyltransf_34 (PF11312)	665 (0.0%)	View
DUF1776 (PF08643)	663 (0.0%)	View
DRE2_N (PF16803)	651 (0.0%)	View
3HCDH_RFF (PF18321)	551 (0.0%)	View
MOLO1 (PF17175)	551 (0.0%)	View
GRDA (PF04723)	481 (0.0%)	View
CmcI (PF04989)	470 (0.0%)	View
DUF5130 (PF17174)	452 (0.0%)	View
Pyr_redox (PF00070)	382 (0.0%)	View
ISPD_C (PF18706)	356 (0.0%)	View
DUF268 (PF03269)	346 (0.0%)	View
Methyltransf_20 (PF12147)	326 (0.0%)	View
HIM1 (PF08732)	323 (0.0%)	View
BpsA_C (PF01861)	322 (0.0%)	View
Methyltransf_17 (PF12692)	240 (0.0%)	View
DUF6094 (PF19587)	230 (0.0%)	View
Methyltrans_Mon (PF14314)	173 (0.0%)	View
UPF0146 (PF03686)	162 (0.0%)	View
DUF5129 (PF17173)	128 (0.0%)	View
DUF166 (PF02593)	123 (0.0%)	View
PARP_regulatory (PF01358)	122 (0.0%)	View
CoV_Methyltr_2 (PF06460)	86 (0.0%)	View
AviRa (PF11599)	79 (0.0%)	View
CoV_ExoN (PF06471)	78 (0.0%)	View
FmrO (PF07091)	54 (0.0%)	View
fvmX7 (PF20005)	49 (0.0%)	View
Pox_mRNA-cap (PF03341)	40 (0.0%)	View
Orbi_VP4 (PF05059)	34 (0.0%)	View
HcgC (PF06690)	20 (0.0%)	View
Reovirus_L2 (PF06016)	18 (0.0%)	View
V_cholerae_RfbT (PF05575)	3 (0.0%)	View
Pyr_redox_3 (PF13738)	0 (0.0%)	View
Thi4 (PF01946)	0 (0.0%)	View
Total: 209	Total: 2755088	No alignment ℹ

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Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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Clan: NADP_Rossmann (CL0063)

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