5859  structures 7128  species 171  interactions 362090  sequences 3669  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 148 families and the total number of domains in the clan is 362090.

Literature references

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

Members

This clan contains the following 148 member families:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N adh_short ADH_zinc_N AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA Bac_GDH Bin3 CheR CMAS CmcI CoA_binding Cons_hypoth95 DAO DapB_N DFP DNA_circ_N DNA_methylase DOT1 DREV DUF1442 DUF166 DUF1776 DUF185 DUF2431 DUF248 DUF268 DUF3321 DUF43 DUF519 DUF548 DUF574 DUF633 DUF752 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 Fibrillarin FMO-like FmrO FtsJ G6PD_N GCD14 GDI GFO_IDH_MocA GIDA GidB GLF Glyco_hydro_4 GMC_oxred_N Gp_dh_N GRDA HI0933_like HIM1 Hydrolase_5 Hydroxy-O-Methy IlvN KR LCM Ldh_1_N Lycopene_cycl Malic_M Mannitol_dh Met_10 Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_15 Methyltransf_16 Methyltransf_2 Methyltransf_3 Methyltransf_4 Methyltransf_5 Methyltransf_8 Methyltransf_9 MethyltransfD12 MetW Mg-por_mtran_C Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS Nol1_Nop2_Fmu NSP13 OCD_Mu_crystall PARP_regulatory PCMT PDH Polysacc_synt_2 Pox_MCEL Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 Saccharop_dh 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 Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 V_cholerae_RfbT

External database links

CATH: 3.40.50.1320
SCOP: 51734

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) 42056 (11.6%) View
Pyr_redox_2 (PF07992) 22777 (6.3%) View
Methyltransf_11 (PF08241) 18330 (5.1%) View
Epimerase (PF01370) 18015 (5.0%) View
ADH_zinc_N (PF00107) 17749 (4.9%) View
Pyr_redox (PF00070) 16651 (4.6%) View
DAO (PF01266) 11806 (3.3%) View
FAD_binding_3 (PF01494) 7484 (2.1%) View
GFO_IDH_MocA (PF01408) 7416 (2.0%) View
2-Hacid_dh_C (PF02826) 7360 (2.0%) View
FAD_binding_2 (PF00890) 6314 (1.7%) View
Gp_dh_N (PF00044) 6230 (1.7%) View
TrkA_N (PF02254) 5358 (1.5%) View
Amino_oxidase (PF01593) 5127 (1.4%) View
MTS (PF05175) 5106 (1.4%) View
NAD_binding_2 (PF03446) 4950 (1.4%) View
ThiF (PF00899) 4746 (1.3%) View
FtsJ (PF01728) 4683 (1.3%) View
Mur_ligase (PF01225) 4678 (1.3%) View
Ldh_1_N (PF00056) 4560 (1.3%) View
Semialdhyde_dh (PF01118) 4032 (1.1%) View
NmrA (PF05368) 3909 (1.1%) View
3HCDH_N (PF02737) 3431 (0.9%) View
GMC_oxred_N (PF00732) 3348 (0.9%) View
CoA_binding (PF02629) 3316 (0.9%) View
Shikimate_DH (PF01488) 3221 (0.9%) View
KR (PF08659) 3125 (0.9%) View
Methyltransf_12 (PF08242) 3117 (0.9%) View
Nol1_Nop2_Fmu (PF01189) 2921 (0.8%) View
N6_Mtase (PF02384) 2860 (0.8%) View
UDPG_MGDP_dh_N (PF03721) 2804 (0.8%) View
DNA_methylase (PF00145) 2679 (0.7%) View
RrnaAD (PF00398) 2648 (0.7%) View
FMO-like (PF00743) 2647 (0.7%) View
F420_oxidored (PF03807) 2626 (0.7%) View
Malic_M (PF03949) 2608 (0.7%) View
tRNA_U5-meth_tr (PF05958) 2577 (0.7%) View
N6_N4_Mtase (PF01555) 2570 (0.7%) View
ELFV_dehydrog (PF00208) 2501 (0.7%) View
GIDA (PF01134) 2329 (0.6%) View
NAD_Gly3P_dh_N (PF01210) 2234 (0.6%) View
NAD_binding_3 (PF03447) 2227 (0.6%) View
THF_DHG_CYH_C (PF02882) 1991 (0.5%) View
AlaDh_PNT_C (PF01262) 1990 (0.5%) View
PrmA (PF06325) 1945 (0.5%) View
G6PD_N (PF00479) 1903 (0.5%) View
RmlD_sub_bind (PF04321) 1767 (0.5%) View
Methyltransf_2 (PF00891) 1763 (0.5%) View
ApbA (PF02558) 1763 (0.5%) View
DapB_N (PF01113) 1754 (0.5%) View
CheR (PF01739) 1739 (0.5%) View
Methyltransf_4 (PF02390) 1731 (0.5%) View
Spermine_synth (PF01564) 1719 (0.5%) View
DFP (PF04127) 1716 (0.5%) View
Ubie_methyltran (PF01209) 1686 (0.5%) View
NAD_binding_4 (PF07993) 1683 (0.5%) View
Methyltransf_3 (PF01596) 1665 (0.5%) View
Methyltransf_5 (PF01795) 1633 (0.5%) View
Cons_hypoth95 (PF03602) 1618 (0.4%) View
CMAS (PF02353) 1615 (0.4%) View
PCMT (PF01135) 1614 (0.4%) View
HI0933_like (PF03486) 1578 (0.4%) View
UPF0020 (PF01170) 1563 (0.4%) View
Saccharop_dh (PF03435) 1551 (0.4%) View
IlvN (PF07991) 1550 (0.4%) View
Methyltrans_SAM (PF10672) 1529 (0.4%) View
GidB (PF02527) 1498 (0.4%) View
PDH (PF02153) 1464 (0.4%) View
Mannitol_dh (PF01232) 1391 (0.4%) View
Polysacc_synt_2 (PF02719) 1346 (0.4%) View
DXP_reductoisom (PF02670) 1337 (0.4%) View
DXP_redisom_C (PF08436) 1334 (0.4%) View
MethyltransfD12 (PF02086) 1295 (0.4%) View
OCD_Mu_crystall (PF02423) 1139 (0.3%) View
AdoHcyase_NAD (PF00670) 1135 (0.3%) View
continued
Pfam family Num. domains Alignment
LCM (PF04072) 1108 (0.3%) View
Methyltransf_16 (PF10294) 1076 (0.3%) View
Thi4 (PF01946) 854 (0.2%) View
Glyco_hydro_4 (PF02056) 853 (0.2%) View
3Beta_HSD (PF01073) 850 (0.2%) View
DUF185 (PF02636) 768 (0.2%) View
Trp_halogenase (PF04820) 744 (0.2%) View
NAD_binding_5 (PF07994) 684 (0.2%) View
DUF752 (PF05430) 648 (0.2%) View
Met_10 (PF02475) 544 (0.2%) View
DUF519 (PF04378) 544 (0.2%) View
TPMT (PF05724) 538 (0.1%) View
Eco57I (PF07669) 529 (0.1%) View
Mqo (PF06039) 526 (0.1%) View
GDI (PF00996) 514 (0.1%) View
DUF548 (PF04445) 514 (0.1%) View
TehB (PF03848) 511 (0.1%) View
Bac_GDH (PF05088) 495 (0.1%) View
DUF633 (PF04816) 478 (0.1%) View
GCD14 (PF08704) 477 (0.1%) View
GLF (PF03275) 470 (0.1%) View
Methyltransf_10 (PF05971) 438 (0.1%) View
Lycopene_cycl (PF05834) 431 (0.1%) View
Methyltransf_9 (PF08003) 420 (0.1%) View
DUF248 (PF03141) 413 (0.1%) View
MT-A70 (PF05063) 385 (0.1%) View
TRM (PF02005) 374 (0.1%) View
rRNA_methylase (PF06962) 357 (0.1%) View
PRMT5 (PF05185) 322 (0.1%) View
Enoyl_reductase (PF12241) 320 (0.1%) View
Eno-Rase_FAD_bd (PF07055) 313 (0.1%) View
Eno-Rase_NADH_b (PF12242) 302 (0.1%) View
MetW (PF07021) 300 (0.1%) View
Fibrillarin (PF01269) 299 (0.1%) View
DUF938 (PF06080) 296 (0.1%) View
Pox_MCEL (PF03291) 295 (0.1%) View
Strep_67kDa_ant (PF06100) 291 (0.1%) View
DUF574 (PF04672) 276 (0.1%) View
Rsm22 (PF09243) 263 (0.1%) View
NSP13 (PF06460) 225 (0.1%) View
DOT1 (PF08123) 217 (0.1%) View
CmcI (PF04989) 214 (0.1%) View
Rossmann-like (PF10727) 212 (0.1%) View
Methyltransf_15 (PF09445) 206 (0.1%) View
N2227 (PF07942) 202 (0.1%) View
SE (PF08491) 194 (0.1%) View
DUF2431 (PF10354) 187 (0.1%) View
Hydroxy-O-Methy (PF05891) 170 (0.0%) View
Mg-por_mtran_C (PF07109) 154 (0.0%) View
Methyltransf_8 (PF05148) 152 (0.0%) View
TRM13 (PF05206) 151 (0.0%) View
Hydrolase_5 (PF12147) 148 (0.0%) View
DNA_circ_N (PF07157) 132 (0.0%) View
N6-adenineMlase (PF10237) 131 (0.0%) View
Bin3 (PF06859) 121 (0.0%) View
NAS (PF03059) 118 (0.0%) View
Prenylcys_lyase (PF07156) 116 (0.0%) View
NodS (PF05401) 116 (0.0%) View
AdoMet_MTase (PF07757) 97 (0.0%) View
NNMT_PNMT_TEMT (PF01234) 97 (0.0%) View
DUF3321 (PF11968) 92 (0.0%) View
GRDA (PF04723) 87 (0.0%) View
PARP_regulatory (PF01358) 84 (0.0%) View
FmrO (PF07091) 78 (0.0%) View
DUF43 (PF01861) 76 (0.0%) View
V_cholerae_RfbT (PF05575) 65 (0.0%) View
DREV (PF05219) 63 (0.0%) View
DUF1776 (PF08643) 60 (0.0%) View
DUF1442 (PF07279) 46 (0.0%) View
UPF0146 (PF03686) 38 (0.0%) View
DUF166 (PF02593) 35 (0.0%) View
DUF268 (PF03269) 28 (0.0%) View
HIM1 (PF08732) 27 (0.0%) View
Total: 148 Total: 362090 Clan alignment
 

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Family relationships

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

Species distribution

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Interactions

There are 171 interactions for this clan. More...

Interacting families
A B
Hydroxy-O-Methy Hydroxy-O-Methy
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
DUF752 DUF752
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
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
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
DXP_reductoisom DXP_redisom_C
Shikimate_DH Shikimate_DH
GlutR_N
Shikimate_dh_N
Thi4 Thi4
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
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
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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