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8681  structures 18998  species 174  interactions 984446  sequences 8330  architectures

Clan: NADP_Rossmann (CL0063)

Summary

FAD/NAD(P)-binding Rossmann fold Superfamily Add an annotation

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 180 families and the total number of domains in the clan is 984446. The clan was built by RD Finn.

Literature references

  1. 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 180 member families:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa Bac_GDH Bin3 CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 DAO DapB_N DFP DNA_circ_N DNA_methylase DOT1 DREV dTMP_synthase DUF1442 DUF1776 DUF2431 DUF268 DUF3321 DUF43 DUF633 DUF938 DXP_redisom_C DXP_reductoisom 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 G-7-MTase G6PD_N GCD14 GDI GFO_IDH_MocA GIDA GidB GLF Glyco_hydro_4 GMC_oxred_N Gp_dh_N GRAS GRDA HI0933_like HIM1 IlvN K_oxygenase KR LCM Ldh_1_N Lycopene_cycl Malic_M Mannitol_dh Met_10 Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 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_26 Methyltransf_27 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_11 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 Nol1_Nop2_Fmu Nol1_Nop2_Fmu_2 NSP13 OCD_Mu_crystall PARP_regulatory PCMT PDH Polysacc_synt_2 Pox_MCEL Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Saccharop_dh SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth Strep_67kDa_ant TehB THF_DHG_CYH_C Thi4 ThiF TPMT TrkA_N TRM TRM13 tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 V_cholerae_RfbT XdhC_C YjeF_N

External database links

Domain organisation

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

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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) 80936 (8.2%) View
Pyr_redox_2 (PF07992) 57441 (5.8%) View
ADH_zinc_N (PF00107) 42002 (4.3%) View
Pyr_redox (PF00070) 40648 (4.1%) View
Epimerase (PF01370) 38903 (4.0%) View
DAO (PF01266) 27418 (2.8%) View
Methyltransf_11 (PF08241) 22723 (2.3%) View
adh_short_C2 (PF13561) 22490 (2.3%) View
GFO_IDH_MocA (PF01408) 20348 (2.1%) View
2-Hacid_dh_C (PF02826) 20266 (2.1%) View
FAD_binding_3 (PF01494) 17997 (1.8%) View
FAD_binding_2 (PF00890) 15429 (1.6%) View
TrkA_N (PF02254) 14934 (1.5%) View
NAD_binding_10 (PF13460) 14495 (1.5%) View
Methyltransf_23 (PF13489) 14355 (1.5%) View
Gp_dh_N (PF00044) 14213 (1.4%) View
Mur_ligase (PF01225) 13732 (1.4%) View
Ldh_1_N (PF00056) 12983 (1.3%) View
NAD_binding_2 (PF03446) 12732 (1.3%) View
ThiF (PF00899) 12207 (1.2%) View
Methyltransf_31 (PF13847) 11527 (1.2%) View
NAD_binding_8 (PF13450) 10693 (1.1%) View
Semialdhyde_dh (PF01118) 10449 (1.1%) View
FtsJ (PF01728) 10200 (1.0%) View
Methyltransf_26 (PF13659) 9512 (1.0%) View
Amino_oxidase (PF01593) 8963 (0.9%) View
Nol1_Nop2_Fmu (PF01189) 8954 (0.9%) View
MTS (PF05175) 8728 (0.9%) View
Methyltransf_18 (PF12847) 8520 (0.9%) View
Shikimate_DH (PF01488) 8457 (0.9%) View
3HCDH_N (PF02737) 8383 (0.9%) View
GMC_oxred_N (PF00732) 7804 (0.8%) View
N6_Mtase (PF02384) 7778 (0.8%) View
DNA_methylase (PF00145) 7421 (0.8%) View
NAD_binding_11 (PF14833) 7339 (0.7%) View
tRNA_U5-meth_tr (PF05958) 7304 (0.7%) View
Pyr_redox_3 (PF13738) 7189 (0.7%) View
UDPG_MGDP_dh_N (PF03721) 7072 (0.7%) View
N6_N4_Mtase (PF01555) 7047 (0.7%) View
Malic_M (PF03949) 6923 (0.7%) View
F420_oxidored (PF03807) 6885 (0.7%) View
KR (PF08659) 6808 (0.7%) View
CoA_binding (PF02629) 6798 (0.7%) View
RrnaAD (PF00398) 6621 (0.7%) View
ELFV_dehydrog (PF00208) 6466 (0.7%) View
GIDA (PF01134) 6402 (0.7%) View
NAD_binding_3 (PF03447) 6031 (0.6%) View
NAD_Gly3P_dh_N (PF01210) 5998 (0.6%) View
THF_DHG_CYH_C (PF02882) 5651 (0.6%) View
AlaDh_PNT_C (PF01262) 5257 (0.5%) View
DapB_N (PF01113) 5206 (0.5%) View
DFP (PF04127) 5121 (0.5%) View
Mannitol_dh (PF01232) 4952 (0.5%) View
G6PD_N (PF00479) 4951 (0.5%) View
ApbA (PF02558) 4828 (0.5%) View
Methyltransf_5 (PF01795) 4779 (0.5%) View
Methyltransf_4 (PF02390) 4759 (0.5%) View
PrmA (PF06325) 4673 (0.5%) View
NmrA (PF05368) 4570 (0.5%) View
Cons_hypoth95 (PF03602) 4548 (0.5%) View
CoA_binding_2 (PF13380) 4531 (0.5%) View
ADH_zinc_N_2 (PF13602) 4473 (0.5%) View
CoA_binding_3 (PF13727) 4439 (0.5%) View
Methyltrans_SAM (PF10672) 4405 (0.4%) View
GidB (PF02527) 4375 (0.4%) View
PDH (PF02153) 4258 (0.4%) View
IlvN (PF07991) 4225 (0.4%) View
CMAS (PF02353) 4148 (0.4%) View
Ubie_methyltran (PF01209) 4079 (0.4%) View
HI0933_like (PF03486) 4052 (0.4%) View
RmlD_sub_bind (PF04321) 4012 (0.4%) View
CheR (PF01739) 3912 (0.4%) View
UPF0020 (PF01170) 3872 (0.4%) View
Methyltransf_3 (PF01596) 3858 (0.4%) View
Spermine_synth (PF01564) 3831 (0.4%) View
Saccharop_dh (PF03435) 3742 (0.4%) View
NAD_binding_4 (PF07993) 3739 (0.4%) View
MethyltransfD12 (PF02086) 3733 (0.4%) View
Polysacc_synt_2 (PF02719) 3666 (0.4%) View
YjeF_N (PF03853) 3610 (0.4%) View
PCMT (PF01135) 3573 (0.4%) View
DXP_reductoisom (PF02670) 3428 (0.3%) View
DXP_redisom_C (PF08436) 3400 (0.3%) View
Methyltransf_2 (PF00891) 3396 (0.3%) View
NAD_binding_7 (PF13241) 3188 (0.3%) View
LCM (PF04072) 3171 (0.3%) View
Methyltransf_12 (PF08242) 3160 (0.3%) View
Glyco_hydro_4 (PF02056) 3002 (0.3%) View
FMO-like (PF00743) 2951 (0.3%) View
OCD_Mu_crystall (PF02423) 2697 (0.3%) View
Methyltransf_21 (PF05050) 2587 (0.3%) View
continued
Pfam family Num. domains Alignment
Methyltransf_16 (PF10294) 2584 (0.3%) View
FAD_oxidored (PF12831) 2577 (0.3%) View
AdoHcyase_NAD (PF00670) 2557 (0.3%) View
XdhC_C (PF13478) 2511 (0.3%) View
Mqo (PF06039) 1946 (0.2%) View
GRAS (PF03514) 1831 (0.2%) View
3Beta_HSD (PF01073) 1802 (0.2%) View
Methyltransf_28 (PF02636) 1692 (0.2%) View
Methyltransf_30 (PF05430) 1653 (0.2%) View
Trp_halogenase (PF04820) 1611 (0.2%) View
DUF633 (PF04816) 1587 (0.2%) View
NAD_binding_9 (PF13454) 1586 (0.2%) View
RsmJ (PF04378) 1570 (0.2%) View
GLF (PF03275) 1461 (0.1%) View
SAM_MT (PF04445) 1454 (0.1%) View
Methyltransf_24 (PF13578) 1368 (0.1%) View
NAD_binding_5 (PF07994) 1323 (0.1%) View
rRNA_methylase (PF06962) 1285 (0.1%) View
Methyltransf_10 (PF05971) 1276 (0.1%) View
TehB (PF03848) 1247 (0.1%) View
Methyltransf_32 (PF13679) 1223 (0.1%) View
Bac_GDH (PF05088) 1221 (0.1%) View
Methyltransf_25 (PF13649) 1216 (0.1%) View
Methyltransf_9 (PF08003) 1216 (0.1%) View
K_oxygenase (PF13434) 1152 (0.1%) View
GCD14 (PF08704) 1145 (0.1%) View
Strep_67kDa_ant (PF06100) 1128 (0.1%) View
GDI (PF00996) 1094 (0.1%) View
Nol1_Nop2_Fmu_2 (PF13636) 1049 (0.1%) View
TPMT (PF05724) 1046 (0.1%) View
Met_10 (PF02475) 1002 (0.1%) View
MT-A70 (PF05063) 995 (0.1%) View
Eco57I (PF07669) 913 (0.1%) View
Methyltransf_27 (PF13708) 854 (0.1%) View
TRM (PF02005) 846 (0.1%) View
Lycopene_cycl (PF05834) 839 (0.1%) View
PRMT5 (PF05185) 750 (0.1%) View
Methyltransf_19 (PF04672) 720 (0.1%) View
Methyltransf_29 (PF03141) 712 (0.1%) View
Methyltransf_7 (PF03492) 707 (0.1%) View
Rsm22 (PF09243) 679 (0.1%) View
Thi4 (PF01946) 671 (0.1%) View
MetW (PF07021) 667 (0.1%) View
Eno-Rase_FAD_bd (PF07055) 659 (0.1%) View
Enoyl_reductase (PF12241) 655 (0.1%) View
Eno-Rase_NADH_b (PF12242) 648 (0.1%) View
Pox_MCEL (PF03291) 647 (0.1%) View
Fibrillarin (PF01269) 616 (0.1%) View
Rossmann-like (PF10727) 557 (0.1%) View
DOT1 (PF08123) 554 (0.1%) View
DUF938 (PF06080) 529 (0.1%) View
Methyltransf_20 (PF12147) 478 (0.0%) View
N2227 (PF07942) 457 (0.0%) View
TylF (PF05711) 452 (0.0%) View
DUF2431 (PF10354) 435 (0.0%) View
SE (PF08491) 429 (0.0%) View
Methyltransf_15 (PF09445) 426 (0.0%) View
NSP13 (PF06460) 426 (0.0%) View
Methyltransf_PK (PF05891) 406 (0.0%) View
G-7-MTase (PF12803) 388 (0.0%) View
DNA_circ_N (PF07157) 365 (0.0%) View
Methyltransf_8 (PF05148) 358 (0.0%) View
N6-adenineMlase (PF10237) 349 (0.0%) View
Prenylcys_lyase (PF07156) 325 (0.0%) View
Bin3 (PF06859) 294 (0.0%) View
CmcI (PF04989) 285 (0.0%) View
FmrO (PF07091) 272 (0.0%) View
TRM13 (PF05206) 265 (0.0%) View
NNMT_PNMT_TEMT (PF01234) 264 (0.0%) View
Methyltransf_22 (PF13383) 252 (0.0%) View
NodS (PF05401) 251 (0.0%) View
AdoMet_MTase (PF07757) 246 (0.0%) View
GRDA (PF04723) 223 (0.0%) View
NAS (PF03059) 220 (0.0%) View
DUF3321 (PF11968) 219 (0.0%) View
Mg-por_mtran_C (PF07109) 218 (0.0%) View
DREV (PF05219) 166 (0.0%) View
DUF43 (PF01861) 163 (0.0%) View
Methyltrans_Mon (PF14314) 144 (0.0%) View
DUF1776 (PF08643) 135 (0.0%) View
PARP_regulatory (PF01358) 111 (0.0%) View
dTMP_synthase (PF02593) 85 (0.0%) View
DUF1442 (PF07279) 79 (0.0%) View
UPF0146 (PF03686) 77 (0.0%) View
DUF268 (PF03269) 72 (0.0%) View
V_cholerae_RfbT (PF05575) 55 (0.0%) View
Methyltransf_17 (PF12692) 51 (0.0%) View
HIM1 (PF08732) 31 (0.0%) View
AviRa (PF11599) 11 (0.0%) View
Total: 180 Total: 984446 Clan alignment
 

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Family relationships

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

We could not retrieve a family relationship diagram for this clan.

Species distribution

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This tree shows the occurrence of the domains in this clan across different species. More...

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Interactions

There are 174 interactions for this clan. More...

Interacting families
A B
Pyr_redox_2 Pyr_redox
Rubredoxin
Rieske
Oxidored_FMN
ETF
DHO_dh
DAO
E3_binding
Pyr_redox_dim
Pyr_redox_2
FCSD-flav_bind
FAD_binding_3 FAD_binding_3
Phe_hydrox_dim
GDI Ras
GDI
PPTA
FAD_binding_2 Fer4
Fer2
FAD_binding_2
Sdh_cyt
Fumarate_red_C
Succ_DH_flav_C
SoxG
Spermine_synth Spermine_synth
Gp_dh_N Gp_dh_N
Gp_dh_C
TehB TehB
GFO_IDH_MocA GFO_IDH_MocA
GFO_IDH_MocA_C
Biliv-reduc_cat
2-Hacid_dh_C 2-Hacid_dh
2-Hacid_dh_C
ADH_zinc_N ADH_zinc_N
ADH_N
N6_N4_Mtase N6_N4_Mtase
Epimerase Formyl_trans_N
Aldose_epim
Epimerase
Formyl_trans_C
FMO-like FMO-like
FtsJ FtsJ
CoA_binding Ligase_CoA
CoA_binding
Put_DNA-bind_N
ATP-grasp_2
adh_short adh_short
PrmA Ribosomal_L11
Ribosomal_L11_N
PrmA
3HCDH_N Thiolase_N
3HCDH
3HCDH_N
NAD_binding_2 6PGD
NAD_binding_2
Glyco_hydro_4 Glyco_hydro_4
DXP_redisom_C DXP_reductoisom
DXP_redisom_C
CmcI CmcI
DapB_N DapB_N
DapB_C
NAD_binding_3 Homoserine_dh
DUF108
NAD_binding_3
NmrA NmrA
PCMT PCMT
Methyltransf_4 WD40
Methyltransf_4
CheR CheR_N
Semialdhyde_dh HMGL-like
Semialdhyde_dh
Semialdhyde_dhC
AcetDehyd-dimer
THF_DHG_CYH_C THF_DHG_CYH
THF_DHG_CYH_C
tRNA_U5-meth_tr TRAM
tRNA_U5-meth_tr
Methyltransf_7 Methyltransf_7
GLF DAO
GLF
UDPG_MGDP_dh_N UDPG_MGDP_dh
UDPG_MGDP_dh_C
UDPG_MGDP_dh_N
PARP_regulatory PARP_regulatory
RmlD_sub_bind RmlD_sub_bind
Methyltransf_PK Methyltransf_PK
DUF43 DUF43
OCD_Mu_crystall OCD_Mu_crystall
Cons_hypoth95 Cons_hypoth95
Nol1_Nop2_Fmu NusB
Nol1_Nop2_Fmu
Mur_ligase Mur_ligase
Mur_ligase_C
Mur_ligase_M
AlaDh_PNT_C AlaDh_PNT_C
AlaDh_PNT_N
DAO DAO
GCV_T
Succ_DH_flav_C
GLF
SoxD
Fer2_BFD
Pyr_redox_2
GCV_T_C
GCD14 GCD14
Trp_halogenase Trp_halogenase
Malic_M malic
Malic_M
MTS RF-1
MTS
MTS_N
DFP DFP
F420_oxidored F420_oxidored
DUF1932
Thi4 Thi4
DXP_reductoisom DXP_redisom_C
Shikimate_DH Shikimate_DH
GlutR_N
Shikimate_dh_N
MethyltransfD12 MethyltransfD12
Ldh_1_N Ldh_1_N
Ldh_1_C
LCM LCM
Fibrillarin Fibrillarin
Nop
ThiF UQ_con
ubiquitin
ThiF
UBACT
ThiS
MoeZ_MoeB
E2_bind
UBA_e1_thiolCys
ELFV_dehydrog ELFV_dehydrog
ELFV_dehydrog_N
Methyltransf_30 Methyltransf_30
TRM TRM
AdoHcyase_NAD AdoHcyase_NAD
AdoHcyase
Met_10 Met_10
Methyltransf_3 Methyltransf_3
PDH PDH
CMAS CMAS
TPMT TPMT
NAD_binding_5 Inos-1-P_synth
NAD_binding_5
TrkA_N TrkA_C
TrkA_N
Saccharop_dh Saccharop_dh
G6PD_N G6PD_N
G6PD_C
Pyr_redox Pyr_redox
DHO_dh
E3_binding
Pyr_redox_dim
Pyr_redox_2
Methyltransf_12 Methyltransf_12
Amino_oxidase Myb_DNA-binding
Amino_oxidase
SWIRM
Methyltransf_2 Methyltransf_2
Dimerisation
YjeF_N Carb_kinase
YjeF_N
NAD_Gly3P_dh_N NAD_Gly3P_dh_N
Octopine_DH
NAD_Gly3P_dh_C
NNMT_PNMT_TEMT NNMT_PNMT_TEMT
ApbA ApbA
ApbA_C
IlvN IlvC
IlvN
GMC_oxred_N GMC_oxred_N
GMC_oxred_C
Polysacc_synt_2 Polysacc_synt_2

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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