tryptophan dehydrogenase ScyB; The tryptophan dehydrogenase (EC 1.4.1.19) ScyB performs a ...
2-343
1.79e-135
tryptophan dehydrogenase ScyB; The tryptophan dehydrogenase (EC 1.4.1.19) ScyB performs a reversible NAD(+)-dependent deamination of L-Trp to 3-indolepyruvate. ScyB occurs in Cyanobacteria that biosynthesize scytonemin, a natural sunscreen, from tryptophan.
The actual alignment was detected with superfamily member NF035922:
Pssm-ID: 411511 [Multi-domain] Cd Length: 346 Bit Score: 389.86 E-value: 1.79e-135
tryptophan dehydrogenase ScyB; The tryptophan dehydrogenase (EC 1.4.1.19) ScyB performs a ...
2-343
1.79e-135
tryptophan dehydrogenase ScyB; The tryptophan dehydrogenase (EC 1.4.1.19) ScyB performs a reversible NAD(+)-dependent deamination of L-Trp to 3-indolepyruvate. ScyB occurs in Cyanobacteria that biosynthesize scytonemin, a natural sunscreen, from tryptophan.
Pssm-ID: 411511 [Multi-domain] Cd Length: 346 Bit Score: 389.86 E-value: 1.79e-135
Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Glutamate ...
2-349
8.20e-100
Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Glutamate dehydrogenase/leucine dehydrogenase is part of the Pathway/BioSystem: Glutamine biosynthesis
Pssm-ID: 440103 [Multi-domain] Cd Length: 411 Bit Score: 301.21 E-value: 8.20e-100
NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine ...
145-344
4.08e-81
NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
Pssm-ID: 133444 Cd Length: 200 Bit Score: 246.35 E-value: 4.08e-81
Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Glutamate, leucine, phenylalanine and ...
229-321
4.48e-28
Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.
Pssm-ID: 214847 [Multi-domain] Cd Length: 102 Bit Score: 105.76 E-value: 4.48e-28
tryptophan dehydrogenase ScyB; The tryptophan dehydrogenase (EC 1.4.1.19) ScyB performs a ...
2-343
1.79e-135
tryptophan dehydrogenase ScyB; The tryptophan dehydrogenase (EC 1.4.1.19) ScyB performs a reversible NAD(+)-dependent deamination of L-Trp to 3-indolepyruvate. ScyB occurs in Cyanobacteria that biosynthesize scytonemin, a natural sunscreen, from tryptophan.
Pssm-ID: 411511 [Multi-domain] Cd Length: 346 Bit Score: 389.86 E-value: 1.79e-135
Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Glutamate ...
2-349
8.20e-100
Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]; Glutamate dehydrogenase/leucine dehydrogenase is part of the Pathway/BioSystem: Glutamine biosynthesis
Pssm-ID: 440103 [Multi-domain] Cd Length: 411 Bit Score: 301.21 E-value: 8.20e-100
NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine ...
145-344
4.08e-81
NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
Pssm-ID: 133444 Cd Length: 200 Bit Score: 246.35 E-value: 4.08e-81
NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine ...
149-342
1.87e-38
NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase; Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parrallel to the others. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
Pssm-ID: 133450 [Multi-domain] Cd Length: 217 Bit Score: 136.91 E-value: 1.87e-38
Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Glutamate, leucine, phenylalanine and ...
229-321
4.48e-28
Glutamate/Leucine/Phenylalanine/Valine dehydrogenase; Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.
Pssm-ID: 214847 [Multi-domain] Cd Length: 102 Bit Score: 105.76 E-value: 4.48e-28
NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Amino acid dehydrogenase (DH) is ...
149-342
2.40e-21
NAD(P) binding domain of glutamate dehydrogenase, subgroup 1; Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha -beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.
Pssm-ID: 133445 [Multi-domain] Cd Length: 227 Bit Score: 91.06 E-value: 2.40e-21
3beta17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; This subgroup includes ...
183-219
1.91e-03
3beta17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; This subgroup includes members identified as 3beta17beta hydroxysteroid dehydrogenase, 20beta hydroxysteroid dehydrogenase, and R-alcohol dehydrogenase. These proteins exhibit the canonical active site tetrad and glycine rich NAD(P)-binding motif of the classical SDRs. 17beta-dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens, and include members of the SDR family. 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 have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. 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) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs.
Pssm-ID: 187600 [Multi-domain] Cd Length: 247 Bit Score: 39.29 E-value: 1.91e-03
classical (c) SDR, subgroup 8; This subgroup has a fairly well conserved active site tetrad ...
179-216
9.35e-03
classical (c) SDR, subgroup 8; This subgroup has a fairly well conserved active site tetrad and domain size of the classical SDRs, but has an atypical NAD-binding motif ([ST]G[GA]XGXXG). 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: 187635 [Multi-domain] Cd Length: 250 Bit Score: 37.31 E-value: 9.35e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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