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Conserved domains on  [gi|991820203|ref|NP_001307037|]
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retinol dehydrogenase 16 isoform 2 [Homo sapiens]

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 ...
 46-160 1.86e-42

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 cd09805:

Pssm-ID: 473865 [Multi-domain]  Cd Length: 281  Bit Score: 142.80  E-value: 1.86e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  46 RRELSYFGVKVAMIEPGYFKTAVTSK-ERFLKSFLEIWDRSSPEVKEAYGEKFVADYKKSAEQMEQKCTQDLSLVTNCME 124
Cdd:cd09805  165 RRELQPWGVKVSIIEPGNFKTGITGNsELWEKQAKKLWERLPPEVKKDYGEDYIDELKNKMLKYCSRASPDLSPVIDSIE 244

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 991820203 125 HALIACHPRTRYSAGWDAKLLYLPMSYMPTFLVDAI 160
Cdd:cd09805  245 HALTSRHPRTRYYPGKDAKLLYIPASYLPTSLSDFL 280
 
Name Accession Description Interval E-value
type2_17beta_HSD-like_SDR_c cd09805
human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs; ...
 46-160 1.86e-42

human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs; 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. This classical-SDR subgroup includes the human proteins: type 2 17beta-HSD, type 6 17beta-HSD, type 2 11beta-HSD, dehydrogenase/reductase SDR family member 9, short-chain dehydrogenase/reductase family 9C member 7, 3-hydroxybutyrate dehydrogenase type 1, and retinol dehydrogenase 5. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes 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 (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in the C-terminal region, 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. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.


Pssm-ID: 187665 [Multi-domain]  Cd Length: 281  Bit Score: 142.80  E-value: 1.86e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  46 RRELSYFGVKVAMIEPGYFKTAVTSK-ERFLKSFLEIWDRSSPEVKEAYGEKFVADYKKSAEQMEQKCTQDLSLVTNCME 124
Cdd:cd09805  165 RRELQPWGVKVSIIEPGNFKTGITGNsELWEKQAKKLWERLPPEVKKDYGEDYIDELKNKMLKYCSRASPDLSPVIDSIE 244

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 991820203 125 HALIACHPRTRYSAGWDAKLLYLPMSYMPTFLVDAI 160
Cdd:cd09805  245 HALTSRHPRTRYYPGKDAKLLYIPASYLPTSLSDFL 280
PRK06182 PRK06182
short chain dehydrogenase; Validated
 39-161 4.26e-08

short chain dehydrogenase; Validated


Pssm-ID: 180448 [Multi-domain]  Cd Length: 273  Bit Score: 51.11  E-value: 4.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  39 EGVRERQRRELSYFGVKVAMIEPGYFKT--AVTSKERFLKSfleiwDRSSPevkeaYGEKFVADYKKSAEQMEQKCTQDL 116
Cdd:PRK06182 154 EGFSDALRLEVAPFGIDVVVIEPGGIKTewGDIAADHLLKT-----SGNGA-----YAEQAQAVAASMRSTYGSGRLSDP 223

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 991820203 117 SLVTNCMEHALIACHPRTRYSAGWDAKLLYLPMSYMPTFLVDAIM 161
Cdd:PRK06182 224 SVIADAISKAVTARRPKTRYAVGFGAKPLIFLRRILPDRAFDRLI 268
 
Name Accession Description Interval E-value
type2_17beta_HSD-like_SDR_c cd09805
human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs; ...
 46-160 1.86e-42

human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs; 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. This classical-SDR subgroup includes the human proteins: type 2 17beta-HSD, type 6 17beta-HSD, type 2 11beta-HSD, dehydrogenase/reductase SDR family member 9, short-chain dehydrogenase/reductase family 9C member 7, 3-hydroxybutyrate dehydrogenase type 1, and retinol dehydrogenase 5. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes 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 (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in the C-terminal region, 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. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.


Pssm-ID: 187665 [Multi-domain]  Cd Length: 281  Bit Score: 142.80  E-value: 1.86e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  46 RRELSYFGVKVAMIEPGYFKTAVTSK-ERFLKSFLEIWDRSSPEVKEAYGEKFVADYKKSAEQMEQKCTQDLSLVTNCME 124
Cdd:cd09805  165 RRELQPWGVKVSIIEPGNFKTGITGNsELWEKQAKKLWERLPPEVKKDYGEDYIDELKNKMLKYCSRASPDLSPVIDSIE 244

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 991820203 125 HALIACHPRTRYSAGWDAKLLYLPMSYMPTFLVDAI 160
Cdd:cd09805  245 HALTSRHPRTRYYPGKDAKLLYIPASYLPTSLSDFL 280
PRK06182 PRK06182
short chain dehydrogenase; Validated
 39-161 4.26e-08

short chain dehydrogenase; Validated


Pssm-ID: 180448 [Multi-domain]  Cd Length: 273  Bit Score: 51.11  E-value: 4.26e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  39 EGVRERQRRELSYFGVKVAMIEPGYFKT--AVTSKERFLKSfleiwDRSSPevkeaYGEKFVADYKKSAEQMEQKCTQDL 116
Cdd:PRK06182 154 EGFSDALRLEVAPFGIDVVVIEPGGIKTewGDIAADHLLKT-----SGNGA-----YAEQAQAVAASMRSTYGSGRLSDP 223

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 991820203 117 SLVTNCMEHALIACHPRTRYSAGWDAKLLYLPMSYMPTFLVDAIM 161
Cdd:PRK06182 224 SVIADAISKAVTARRPKTRYAVGFGAKPLIFLRRILPDRAFDRLI 268
PRK05993 PRK05993
SDR family oxidoreductase;
39-163 7.46e-06

SDR family oxidoreductase;


Pssm-ID: 180343 [Multi-domain]  Cd Length: 277  Bit Score: 44.63  E-value: 7.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  39 EGVRERQRRELSYFGVKVAMIEPGYFKTAVTSKErfLKSFLEIWD-RSSPEvKEAY--------GEKFVADYKKSAEQme 109
Cdd:PRK05993 156 EGLSLTLRMELQGSGIHVSLIEPGPIETRFRANA--LAAFKRWIDiENSVH-RAAYqqqmarleGGGSKSRFKLGPEA-- 230

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 991820203 110 qkctqdlslVTNCMEHALIACHPRTRYSAGWDAKLLYLPMSYMPTFLVDAIMYW 163
Cdd:PRK05993 231 ---------VYAVLLHALTAPRPRPHYRVTTPAKQGALLKRLLPARWLYRLLRK 275
PRK06179 PRK06179
short chain dehydrogenase; Provisional
 39-159 1.59e-05

short chain dehydrogenase; Provisional


Pssm-ID: 235725 [Multi-domain]  Cd Length: 270  Bit Score: 43.74  E-value: 1.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  39 EGVRERQRRELSYFGVKVAMIEPGYFKTavtskerflkSFleiwDRSSPEVKEAygekfVADYKKSAEQMEQkctqdlsL 118
Cdd:PRK06179 153 EGYSESLDHEVRQFGIRVSLVEPAYTKT----------NF----DANAPEPDSP-----LAEYDRERAVVSK-------A 206

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 991820203 119 VTNCMEH-------------ALIACHPRTRYSAGWDAKLLYLPMSYMPTFLVDA 159
Cdd:PRK06179 207 VAKAVKKadapevvadtvvkAALGPWPKMRYTAGGQASLLSKLRRFMPAGAVDK 260
PRK06914 PRK06914
SDR family oxidoreductase;
39-153 4.44e-05

SDR family oxidoreductase;


Pssm-ID: 180744 [Multi-domain]  Cd Length: 280  Bit Score: 42.32  E-value: 4.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  39 EGVRERQRRELSYFGVKVAMIEPGYFKTAVTSKErflKSFLEIW-DRSSPevKEAYGEKFVADYKKSAEQmeqkcTQDLS 117
Cdd:PRK06914 161 EGFSESLRLELKPFGIDVALIEPGSYNTNIWEVG---KQLAENQsETTSP--YKEYMKKIQKHINSGSDT-----FGNPI 230

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 991820203 118 LVTNCMEHALIACHPRTRYSAGWDAKLLYLPMSYMP 153
Cdd:PRK06914 231 DVANLIVEIAESKRPKLRYPIGKGVKLMILAKKILP 266
17beta-HSD-like_SDR_c cd05374
17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; 17beta-hydroxysteroid ...
 39-143 7.39e-04

17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes 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 (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) 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. Extended SDRs have additional elements in the C-terminal region, 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. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction.


Pssm-ID: 187632 [Multi-domain]  Cd Length: 248  Bit Score: 38.75  E-value: 7.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 991820203  39 EGVRERQRRELSYFGVKVAMIEPGYFKTAVTSKERflksfleIWDRSSPEvkeaygekfVADYKKSAEQMEQKCTQDLSL 118
Cdd:cd05374  154 EALSESLRLELAPFGIKVTIIEPGPVRTGFADNAA-------GSALEDPE---------ISPYAPERKEIKENAAGVGSN 217

                         90       100       110
                 ....*....|....*....|....*....|.
gi 991820203 119 ------VTNCMEHALIACHPRTRYSAGWDAK 143
Cdd:cd05374  218 pgdpekVADVIVKALTSESPPLRYFLGSDAL 248
PRK08263 PRK08263
short chain dehydrogenase; Provisional
 39-108 7.29e-03

short chain dehydrogenase; Provisional


Pssm-ID: 181334 [Multi-domain]  Cd Length: 275  Bit Score: 35.78  E-value: 7.29e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 991820203  39 EGVRERQRRELSYFGVKVAMIEPGYFKT--AVTSKERFLKsfLEIWDRSSPEVKEAYGEK-FVADYKKSAEQM 108
Cdd:PRK08263 157 EGMSEALAQEVAEFGIKVTLVEPGGYSTdwAGTSAKRATP--LDAYDTLREELAEQWSERsVDGDPEAAAEAL 227
 
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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