L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; ...
6-316
5.30e-150
L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. Members of this subfamily with known structures such as the HicDH of Lactobacillus confusus, the non-allosteric LDH of Lactobacillus pentosus, and the allosteric LDH of Bacillus stearothermophilus, show that they exist as homotetramers. The HicDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
:
Pssm-ID: 133427 [Multi-domain] Cd Length: 306 Bit Score: 423.42 E-value: 5.30e-150
L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; ...
6-316
5.30e-150
L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. Members of this subfamily with known structures such as the HicDH of Lactobacillus confusus, the non-allosteric LDH of Lactobacillus pentosus, and the allosteric LDH of Bacillus stearothermophilus, show that they exist as homotetramers. The HicDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133427 [Multi-domain] Cd Length: 306 Bit Score: 423.42 E-value: 5.30e-150
L-lactate dehydrogenase; This model represents the NAD-dependent L-lactate dehydrogenases from ...
10-312
3.97e-113
L-lactate dehydrogenase; This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of malate dehydrogenases. [Energy metabolism, Anaerobic, Energy metabolism, Glycolysis/gluconeogenesis]
Pssm-ID: 273796 [Multi-domain] Cd Length: 299 Bit Score: 329.55 E-value: 3.97e-113
lactate/malate dehydrogenase, NAD binding domain; L-lactate dehydrogenases are metabolic ...
6-149
1.45e-32
lactate/malate dehydrogenase, NAD binding domain; L-lactate dehydrogenases are metabolic enzymes which catalyze the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyze the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold.
Pssm-ID: 395010 [Multi-domain] Cd Length: 141 Bit Score: 117.71 E-value: 1.45e-32
L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; ...
6-316
5.30e-150
L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases; L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. Members of this subfamily with known structures such as the HicDH of Lactobacillus confusus, the non-allosteric LDH of Lactobacillus pentosus, and the allosteric LDH of Bacillus stearothermophilus, show that they exist as homotetramers. The HicDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133427 [Multi-domain] Cd Length: 306 Bit Score: 423.42 E-value: 5.30e-150
L-lactate dehydrogenase; This model represents the NAD-dependent L-lactate dehydrogenases from ...
10-312
3.97e-113
L-lactate dehydrogenase; This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of malate dehydrogenases. [Energy metabolism, Anaerobic, Energy metabolism, Glycolysis/gluconeogenesis]
Pssm-ID: 273796 [Multi-domain] Cd Length: 299 Bit Score: 329.55 E-value: 3.97e-113
A subgroup of L-lactate dehydrogenases; L-lactate dehydrogenases (LDH) are tetrameric enzymes ...
7-317
3.62e-101
A subgroup of L-lactate dehydrogenases; L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed predominantly of bacterial LDHs and a few fungal LDHs. Bacterial LDHs may be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133428 [Multi-domain] Cd Length: 308 Bit Score: 299.41 E-value: 3.62e-101
L-lactate dehydrogenase-like enzymes; Members of this subfamily are tetrameric NAD-dependent ...
8-315
2.06e-98
L-lactate dehydrogenase-like enzymes; Members of this subfamily are tetrameric NAD-dependent 2-hydroxycarboxylate dehydrogenases including LDHs, L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and LDH-like malate dehydrogenases (MDH). Dehydrogenases catalyze the conversion of carbonyl compounds to alcohols or amino acids. LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. L-HicDH catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133418 [Multi-domain] Cd Length: 300 Bit Score: 292.25 E-value: 2.06e-98
A subgroup of L-lactate dehydrogenases; L-lactate dehydrogenases (LDH) are tetrameric enzymes ...
7-287
4.23e-83
A subgroup of L-lactate dehydrogenases; L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of some bacterial LDHs from firmicutes, gammaproteobacteria, and actinobacteria. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133426 [Multi-domain] Cd Length: 307 Bit Score: 253.41 E-value: 4.23e-83
A subgroup of L-lactate dehydrogenases; L-lactate dehydrogenases (LDH) are tetrameric enzymes ...
7-306
9.89e-71
A subgroup of L-lactate dehydrogenases; L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of eukaryotic LDHs. Vertebrate LDHs are non-allosteric. This is in contrast to some bacterial LDHs that are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133429 [Multi-domain] Cd Length: 312 Bit Score: 222.09 E-value: 9.89e-71
L-lactate dehydrogenase-like malate dehydrogenase proteins; Members of this subfamily have an ...
8-287
1.65e-62
L-lactate dehydrogenase-like malate dehydrogenase proteins; Members of this subfamily have an LDH-like structure and an MDH enzymatic activity. Some members, like MJ0490 from Methanococcus jannaschii, exhibit both MDH and LDH activities. Tetrameric MDHs, including those from phototrophic bacteria, are more similar to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133424 [Multi-domain] Cd Length: 300 Bit Score: 200.39 E-value: 1.65e-62
NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Members ...
8-315
4.25e-45
NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family; Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133419 [Multi-domain] Cd Length: 263 Bit Score: 154.40 E-value: 4.25e-45
A lactate dehydrogenases-like structure with malate dehydrogenase enzymatic activity; The ...
7-312
2.56e-41
A lactate dehydrogenases-like structure with malate dehydrogenase enzymatic activity; The LDH-like MDH proteins have a lactate dehyhydrogenase-like (LDH-like) structure and malate dehydrogenase (MDH) enzymatic activity. This subgroup is composed of some archaeal LDH-like MDHs that prefer NADP(H) rather than NAD(H) as a cofactor. One member, MJ0490 from Methanococcus jannaschii, has been observed to form dimers and tetramers during crystalization, although it is believed to exist primarilly as a tetramer in solution. In addition to its MDH activity, MJ0490 also possesses fructose-1,6-bisphosphate-activated LDH activity. Members of this subgroup have a higher sequence similarity to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)- binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Pssm-ID: 133430 [Multi-domain] Cd Length: 309 Bit Score: 146.01 E-value: 2.56e-41
lactate/malate dehydrogenase, NAD binding domain; L-lactate dehydrogenases are metabolic ...
6-149
1.45e-32
lactate/malate dehydrogenase, NAD binding domain; L-lactate dehydrogenases are metabolic enzymes which catalyze the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyze the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold.
Pssm-ID: 395010 [Multi-domain] Cd Length: 141 Bit Score: 117.71 E-value: 1.45e-32
lactate/malate dehydrogenase, alpha/beta C-terminal domain; L-lactate dehydrogenases are ...
152-287
2.80e-20
lactate/malate dehydrogenase, alpha/beta C-terminal domain; L-lactate dehydrogenases are metabolic enzymes which catalyze the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyze the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes.
Pssm-ID: 397136 Cd Length: 173 Bit Score: 86.26 E-value: 2.80e-20
(3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Beta oxidation of fatty acids ...
4-124
1.70e-03
(3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs; Beta oxidation of fatty acids in eukaryotes occurs by a four-reaction cycle, that may take place in mitochondria or in peroxisomes. (3R)-hydroxyacyl-CoA dehydrogenase is part of rat peroxisomal multifunctional MFE-2, it is a member of the NAD-dependent SDRs, but contains an additional small C-terminal domain that completes the active site pocket and participates in dimerization. The atypical, additional C-terminal extension allows for more extensive dimerization contact than other SDRs. MFE-2 catalyzes the second and third reactions of the peroxisomal beta oxidation cycle. Proteins in this subgroup have a typical catalytic triad, but have a His in place of the usual upstream Asn. This subgroup also contains members identified as 17-beta-hydroxysteroid dehydrogenases, including human peroxisomal 17-beta-hydroxysteroid dehydrogenase type 4 (17beta-HSD type 4, aka MFE-2, encoded by HSD17B4 gene) which is involved in fatty acid beta-oxidation and steroid metabolism. This subgroup also includes two SDR domains of the Neurospora crassa and Saccharomyces cerevisiae multifunctional beta-oxidation protein (MFP, aka Fox2). 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: 187611 [Multi-domain] Cd Length: 250 Bit Score: 39.23 E-value: 1.70e-03
ThiF family; This domain is found in ubiquitin activating E1 family and members of the ...
2-80
5.20e-03
ThiF family; This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1.
Pssm-ID: 459987 [Multi-domain] Cd Length: 238 Bit Score: 37.62 E-value: 5.20e-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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