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Conserved domains on  [gi|769928393|ref|WP_045062596|]
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NAD(P)H-binding protein [Photobacterium leiognathi]

Protein Classification

Rossmann-fold NAD(P)-binding domain-containing protein( domain architecture ID 229380)

Rossmann-fold NAD(P)-binding domain-containing protein may function as an oxidoreductase

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
NADB_Rossmann super family cl21454
Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a ...
6-204 1.23e-67

Rossmann-fold NAD(P)(+)-binding proteins; A large family of proteins that share a Rossmann-fold NAD(P)H/NAD(P)(+) binding (NADB) domain. The NADB domain is found in numerous dehydrogenases of metabolic pathways such as glycolysis, and many other redox enzymes. NAD binding involves numerous hydrogen-bonds and van der Waals contacts, in particular H-bonding of residues in a turn between the first strand and the subsequent helix of the Rossmann-fold topology. Characteristically, this turn exhibits a consensus binding pattern similar to GXGXXG, in which the first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand. Typically, proteins in this family contain a second domain in addition to the NADB domain, which is responsible for specifically binding a substrate and catalyzing a particular enzymatic reaction.


The actual alignment was detected with superfamily member cd05250:

Pssm-ID: 473865 [Multi-domain]  Cd Length: 214  Bit Score: 207.15  E-value: 1.23e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   6 LSAIIAGASGLVGHELLNQLLDNKAFSHIYALSRRELPL--RSSKLQQIIDPLLRINEWEESAPAPTYGFICLGTTKKQA 83
Cdd:cd05250    1 KTALVLGATGLVGKHLLRELLKSPYYSKVTAIVRRKLTFpeAKEKLVQIVVDFERLDEYLEAFQNPDVGFCCLGTTRKKA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  84 GSKAGLAAVDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPSHYLRCKGKMEQAINNMGFDNCIFIRPGPLKGERSQIR 163
Cdd:cd05250   81 GSQENFRKVDHDYVLKLAKLAKAAGVQHFLLVSSLGADPKSSFLYLKVKGEVERDLQKLGFERLTIFRPGLLLGERQESR 160
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 769928393 164 HDEQLLQQVFDLINPLVIGPLKhfsPIPAECVARSMVKMAL 204
Cdd:cd05250  161 PGERLAQKLLRILSPLGFPKYK---PIPAETVAKAMVKAAL 198
 
Name Accession Description Interval E-value
CC3_like_SDR_a cd05250
CC3(TIP30)-like, atypical (a) SDRs; Atypical SDRs in this subgroup include CC3 (also known as ...
6-204 1.23e-67

CC3(TIP30)-like, atypical (a) SDRs; Atypical SDRs in this subgroup include CC3 (also known as TIP30) which is implicated in tumor suppression. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine rich NAD(P)-binding motif that resembles the extended SDRs, and have an active site triad of the SDRs (YXXXK and upstream Ser), although the upstream Asn of the usual SDR active site is substituted with Asp. For CC3, the Tyr of the triad is displaced compared to the usual SDRs and the protein is monomeric, both these observations suggest that the usual SDR catalytic activity is not present. NADP appears to serve an important role as a ligand, and may be important in the interaction with other macromolecules. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187560 [Multi-domain]  Cd Length: 214  Bit Score: 207.15  E-value: 1.23e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   6 LSAIIAGASGLVGHELLNQLLDNKAFSHIYALSRRELPL--RSSKLQQIIDPLLRINEWEESAPAPTYGFICLGTTKKQA 83
Cdd:cd05250    1 KTALVLGATGLVGKHLLRELLKSPYYSKVTAIVRRKLTFpeAKEKLVQIVVDFERLDEYLEAFQNPDVGFCCLGTTRKKA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  84 GSKAGLAAVDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPSHYLRCKGKMEQAINNMGFDNCIFIRPGPLKGERSQIR 163
Cdd:cd05250   81 GSQENFRKVDHDYVLKLAKLAKAAGVQHFLLVSSLGADPKSSFLYLKVKGEVERDLQKLGFERLTIFRPGLLLGERQESR 160
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 769928393 164 HDEQLLQQVFDLINPLVIGPLKhfsPIPAECVARSMVKMAL 204
Cdd:cd05250  161 PGERLAQKLLRILSPLGFPKYK---PIPAETVAKAMVKAAL 198
YbjT COG0702
Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General ...
10-205 8.87e-12

Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General function prediction only];


Pssm-ID: 440466 [Multi-domain]  Cd Length: 215  Bit Score: 62.17  E-value: 8.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  10 IAGASGLVGHELLNQLLDNKAfsHIYALSRRElplrsSKLQQIIDP--------LLRINEWEEsAPAPTYGFICLgttkk 81
Cdd:COG0702    4 VTGATGFIGRRVVRALLARGH--PVRALVRDP-----EKAAALAAAgvevvqgdLDDPESLAA-ALAGVDAVFLL----- 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  82 QAGSKAGLAAVDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPSHYLRCKGKMEQAINNMGFDnCIFIRPGplkgersQ 161
Cdd:COG0702   71 VPSGPGGDFAVDVEGARNLADAAKAAGVKRIVYLSALGADRDSPSPYLRAKAAVEEALRASGLP-YTILRPG-------W 142
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 769928393 162 IrhDEQLLQQVFDLINPLVI---GPLKHFSPIPAECVARSMVKMALA 205
Cdd:COG0702  143 F--MGNLLGFFERLRERGVLplpAGDGRVQPIAVRDVAEAAAAALTD 187
NAD_binding_10 pfam13460
NAD(P)H-binding;
12-167 7.53e-08

NAD(P)H-binding;


Pssm-ID: 463885 [Multi-domain]  Cd Length: 183  Bit Score: 50.68  E-value: 7.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   12 GASGLVGHELLNQLLDNKAfsHIYALSRRElplrsSKLQQIIDP---------LLRINEWEEsAPAPTYG-FICLGTTKK 81
Cdd:pfam13460   1 GATGKIGRLLVKQLLARGH--EVTALVRNP-----EKLADLEDHpgvevvdgdVLDPDDLAE-ALAGQDAvISALGGGGT 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   82 qagskaglaavDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPS-----------HYLRCKGKMEQAINNMGFDnCIFI 150
Cdd:pfam13460  73 -----------DETGAKNIIDAAKAAGVKRFVLVSSLGVGDEVPGpfgpwnkemlgPYLAAKRAAEELLRASGLD-YTIV 140
                         170
                  ....*....|....*...
gi 769928393  151 RPGPLK-GERSQIRHDEQ 167
Cdd:pfam13460 141 RPGWLTdGPTTGYRVTGK 158
 
Name Accession Description Interval E-value
CC3_like_SDR_a cd05250
CC3(TIP30)-like, atypical (a) SDRs; Atypical SDRs in this subgroup include CC3 (also known as ...
6-204 1.23e-67

CC3(TIP30)-like, atypical (a) SDRs; Atypical SDRs in this subgroup include CC3 (also known as TIP30) which is implicated in tumor suppression. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine rich NAD(P)-binding motif that resembles the extended SDRs, and have an active site triad of the SDRs (YXXXK and upstream Ser), although the upstream Asn of the usual SDR active site is substituted with Asp. For CC3, the Tyr of the triad is displaced compared to the usual SDRs and the protein is monomeric, both these observations suggest that the usual SDR catalytic activity is not present. NADP appears to serve an important role as a ligand, and may be important in the interaction with other macromolecules. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187560 [Multi-domain]  Cd Length: 214  Bit Score: 207.15  E-value: 1.23e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   6 LSAIIAGASGLVGHELLNQLLDNKAFSHIYALSRRELPL--RSSKLQQIIDPLLRINEWEESAPAPTYGFICLGTTKKQA 83
Cdd:cd05250    1 KTALVLGATGLVGKHLLRELLKSPYYSKVTAIVRRKLTFpeAKEKLVQIVVDFERLDEYLEAFQNPDVGFCCLGTTRKKA 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  84 GSKAGLAAVDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPSHYLRCKGKMEQAINNMGFDNCIFIRPGPLKGERSQIR 163
Cdd:cd05250   81 GSQENFRKVDHDYVLKLAKLAKAAGVQHFLLVSSLGADPKSSFLYLKVKGEVERDLQKLGFERLTIFRPGLLLGERQESR 160
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 769928393 164 HDEQLLQQVFDLINPLVIGPLKhfsPIPAECVARSMVKMAL 204
Cdd:cd05250  161 PGERLAQKLLRILSPLGFPKYK---PIPAETVAKAMVKAAL 198
SDR_e_a cd05226
Extended (e) and atypical (a) SDRs; Extended or atypical short-chain dehydrogenases/reductases ...
8-158 2.19e-13

Extended (e) and atypical (a) SDRs; Extended or atypical short-chain dehydrogenases/reductases (SDRs, aka tyrosine-dependent oxidoreductases) are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187537 [Multi-domain]  Cd Length: 176  Bit Score: 65.89  E-value: 2.19e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   8 AIIAGASGLVGHELLNQLLDnkAFSHIYALSRRELPLRSSKLQQIIDPLLRINeWEESAPAPTYG----FICLGTTkkqa 83
Cdd:cd05226    1 ILILGATGFIGRALARELLE--QGHEVTLLVRNTKRLSKEDQEPVAVVEGDLR-DLDSLSDAVQGvdvvIHLAGAP---- 73
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  84 GSKAGLAAVDLDLVKDVATTMRNIGVQHIIVISSLGA--------CPRSPSHYLRCKGKMEQAINNMGFDnCIFIRPGPL 155
Cdd:cd05226   74 RDTRDFCEVDVEGTRNVLEAAKEAGVKHFIFISSLGAygdlheetEPSPSSPYLAVKAKTEAVLREASLP-YTIVRPGVI 152

                 ...
gi 769928393 156 KGE 158
Cdd:cd05226  153 YGD 155
YbjT COG0702
Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General ...
10-205 8.87e-12

Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General function prediction only];


Pssm-ID: 440466 [Multi-domain]  Cd Length: 215  Bit Score: 62.17  E-value: 8.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  10 IAGASGLVGHELLNQLLDNKAfsHIYALSRRElplrsSKLQQIIDP--------LLRINEWEEsAPAPTYGFICLgttkk 81
Cdd:COG0702    4 VTGATGFIGRRVVRALLARGH--PVRALVRDP-----EKAAALAAAgvevvqgdLDDPESLAA-ALAGVDAVFLL----- 70
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  82 QAGSKAGLAAVDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPSHYLRCKGKMEQAINNMGFDnCIFIRPGplkgersQ 161
Cdd:COG0702   71 VPSGPGGDFAVDVEGARNLADAAKAAGVKRIVYLSALGADRDSPSPYLRAKAAVEEALRASGLP-YTILRPG-------W 142
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 769928393 162 IrhDEQLLQQVFDLINPLVI---GPLKHFSPIPAECVARSMVKMALA 205
Cdd:COG0702  143 F--MGNLLGFFERLRERGVLplpAGDGRVQPIAVRDVAEAAAAALTD 187
SDR_a5 cd05243
atypical (a) SDRs, subgroup 5; This subgroup contains atypical SDRs, some of which are ...
10-155 4.33e-10

atypical (a) SDRs, subgroup 5; This subgroup contains atypical SDRs, some of which are identified as putative NAD(P)-dependent epimerases, one as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is very similar to the extended SDRs, GXXGXXG, and binds NADP. Generally, this subgroup has poor conservation of the active site tetrad; however, individual sequences do contain matches to the YXXXK active site motif, the upstream Ser, and there is a highly conserved Asp in place of the usual active site Asn throughout the subgroup. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187554 [Multi-domain]  Cd Length: 203  Bit Score: 57.25  E-value: 4.33e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  10 IAGASGLVGHELLNQLLDNKafSHIYALSRRELP---LRSSKLQQIIDPLLRINEWEESAPAPTYGFICLGTTKKQAGSK 86
Cdd:cd05243    4 VVGATGKVGRHVVRELLDRG--YQVRALVRDPSQaekLEAAGAEVVVGDLTDAESLAAALEGIDAVISAAGSGGKGGPRT 81
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 769928393  87 AglaAVDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPS-----HYLRCKGKMEQAINNMGFDNCIfIRPGPL 155
Cdd:cd05243   82 E---AVDYDGNINLIDAAKKAGVKRFVLVSSIGADKPSHPlealgPYLDAKRKAEDYLRASGLDYTI-VRPGGL 151
NDUFA9_like_SDR_a cd05271
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, ...
8-158 5.29e-09

NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs; This subgroup of extended SDR-like proteins are atypical SDRs. They have a glycine-rich NAD(P)-binding motif similar to the typical SDRs, GXXGXXG, and have the YXXXK active site motif (though not the other residues of the SDR tetrad). Members identified include NDUFA9 (mitochondrial) and putative nucleoside-diphosphate-sugar epimerase. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187579 [Multi-domain]  Cd Length: 273  Bit Score: 54.94  E-value: 5.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   8 AIIAGASGLVGHELLNQLLdnKAFSHIYALSRRELPLRSSK----LQQI------------IDPLLR-----INeweesa 66
Cdd:cd05271    3 VTVFGATGFIGRYVVNRLA--KRGSQVIVPYRCEAYARRLLvmgdLGQVlfvefdlrddesIRKALEgsdvvIN------ 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  67 paptygfiCLGT---TKKQagskaGLAAVDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPSHYLRCKGKMEQAINNMg 143
Cdd:cd05271   75 --------LVGRlyeTKNF-----SFEDVHVEGPERLAKAAKEAGVERLIHISALGADANSPSKYLRSKAEGEEAVREA- 140
                        170
                 ....*....|....*
gi 769928393 144 FDNCIFIRPGPLKGE 158
Cdd:cd05271  141 FPEATIVRPSVVFGR 155
NAD_binding_10 pfam13460
NAD(P)H-binding;
12-167 7.53e-08

NAD(P)H-binding;


Pssm-ID: 463885 [Multi-domain]  Cd Length: 183  Bit Score: 50.68  E-value: 7.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   12 GASGLVGHELLNQLLDNKAfsHIYALSRRElplrsSKLQQIIDP---------LLRINEWEEsAPAPTYG-FICLGTTKK 81
Cdd:pfam13460   1 GATGKIGRLLVKQLLARGH--EVTALVRNP-----EKLADLEDHpgvevvdgdVLDPDDLAE-ALAGQDAvISALGGGGT 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   82 qagskaglaavDLDLVKDVATTMRNIGVQHIIVISSLGACPRSPS-----------HYLRCKGKMEQAINNMGFDnCIFI 150
Cdd:pfam13460  73 -----------DETGAKNIIDAAKAAGVKRFVLVSSLGVGDEVPGpfgpwnkemlgPYLAAKRAAEELLRASGLD-YTIV 140
                         170
                  ....*....|....*...
gi 769928393  151 RPGPLK-GERSQIRHDEQ 167
Cdd:pfam13460 141 RPGWLTdGPTTGYRVTGK 158
5beta-POR_like_SDR_a cd08948
progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs; 5beta-POR ...
7-44 8.18e-08

progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs; 5beta-POR catalyzes the reduction of progesterone to 5beta-pregnane-3,20-dione in Digitalis plants. This subgroup of atypical-extended SDRs, shares the structure of an extended SDR, but has a different glycine-rich nucleotide binding motif (GXXGXXG) and lacks the YXXXK active site motif of classical and extended SDRs. Tyr-179 and Lys 147 are present in the active site, but not in the usual SDR configuration. Given these differences, it has been proposed that this subfamily represents a new SDR class. Other atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187652 [Multi-domain]  Cd Length: 308  Bit Score: 51.48  E-value: 8.18e-08
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 769928393   7 SAIIAGASGLVGHELLNQLLDNK-AFSHIYALSRRELPL 44
Cdd:cd08948    1 VALVVGATGISGWALVEHLLSDPgTWWKVYGLSRRPLPT 39
NmrA_TMR_like_1_SDR_a cd05231
NmrA (a transcriptional regulator) and triphenylmethane reductase (TMR) like proteins, ...
100-153 1.06e-04

NmrA (a transcriptional regulator) and triphenylmethane reductase (TMR) like proteins, subgroup 1, atypical (a) SDRs; Atypical SDRs related to NMRa, TMR, and HSCARG (an NADPH sensor). This subgroup resembles the SDRs and has a partially conserved characteristic [ST]GXXGXXG NAD-binding motif, but lacks the conserved active site residues. NmrA is a negative transcriptional regulator of various fungi, involved in the post-translational modulation of the GATA-type transcription factor AreA. NmrA lacks the canonical GXXGXXG NAD-binding motif and has altered residues at the catalytic triad, including a Met instead of the critical Tyr residue. NmrA may bind nucleotides but appears to lack any dehydrogenase activity. HSCARG has been identified as a putative NADP-sensing molecule, and redistributes and restructures in response to NADPH/NADP ratios. Like NmrA, it lacks most of the active site residues of the SDR family, but has an NAD(P)-binding motif similar to the extended SDR family, GXXGXXG. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Atypical SDRs are distinct from classical SDRs. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187542 [Multi-domain]  Cd Length: 259  Bit Score: 42.31  E-value: 1.06e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 769928393 100 VATTMRNIGVQHIIVISSLGACPRSPSHYLRCKGKMEQAINNMGfDNCIFIRPG 153
Cdd:cd05231   89 FASALREAGVKRVVNLSSVGADPESPSGLIRGHWLMEQVLNWAG-LPVVHLRPA 141
MupV_like_SDR_e cd05263
Pseudomonas fluorescens MupV-like, extended (e) SDRs; This subgroup of extended SDR family ...
10-201 1.39e-04

Pseudomonas fluorescens MupV-like, extended (e) SDRs; This subgroup of extended SDR family domains have the characteristic active site tetrad and a well-conserved NAD(P)-binding motif. This subgroup is not well characterized, its members are annotated as having a variety of putative functions. One characterized member is Pseudomonas fluorescens MupV a protein involved in the biosynthesis of Mupirocin, a polyketide-derived antibiotic. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.


Pssm-ID: 187573 [Multi-domain]  Cd Length: 293  Bit Score: 41.97  E-value: 1.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  10 IAGASGLVGHELLNQLLDNKAfsHIYALSRRElplRSSKLQQiidpllRINEWEESAPAPTY--GFICL-------GTTK 80
Cdd:cd05263    3 VTGGTGFLGRHLVKRLLENGF--KVLVLVRSE---SLGEAHE------RIEEAGLEADRVRVleGDLTQpnlglsaAASR 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393  81 KQAGSKAG---LAAV-DLDLVKDVATT------------MRNIGVQHIIVISSLGAC-PRS--------------PSHYL 129
Cdd:cd05263   72 ELAGKVDHvihCAASyDFQAPNEDAWRtnidgtehvlelAARLDIQRFHYVSTAYVAgNREgniretelnpgqnfKNPYE 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393 130 RCKGKMEQAINN-MGFDNCIFIRPGPLKGErSQIRHDEQL--LQQVFDLIN------PLVIGPLKHFSPIPAECVARSMV 200
Cdd:cd05263  152 QSKAEAEQLVRAaATQIPLTVYRPSIVVGD-SKTGRIEKIdgLYELLNLLAklgrwlPMPGNKGARLNLVPVDYVADAIV 230

                 .
gi 769928393 201 K 201
Cdd:cd05263  231 Y 231
HIM1 pfam08732
HIM1; HIM1 (high induction of mutagenesis protein 1) plays a role in the control of ...
74-158 6.95e-04

HIM1; HIM1 (high induction of mutagenesis protein 1) plays a role in the control of spontaneous and induced mutagenesis. It is thought to participate in the control of processing of mutational intermediates appearing during error-prone bypass of DNA damage.


Pssm-ID: 400878  Cd Length: 169  Bit Score: 38.84  E-value: 6.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 769928393   74 IC-LGTTKKQA-GSKAGLAAVDLDLVKDVATTMRNIGVQHIIVISSLG-ACPRSPSHYLRCKGKMEQAINNM---GFDNC 147
Cdd:pfam08732  52 IStLGSTSHSAkKSNTPRNFVDYDLNFQLAQTFANTEDKKLVIVTSFNnKLLSHVSPYFRTKMKLENDLQNKlppKLKEL 131
                          90
                  ....*....|.
gi 769928393  148 IFIRPGPLKGE 158
Cdd:pfam08732 132 VILRPGPLVGN 142
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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