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Literature summary for 1.14.13.33 extracted from

  • Westphal, A.H.; Tischler, D.; Heinke, F.; Hofmann, S.; Groening, J.A.D.; Labudde, D.; van Berkel, W.J.H.
    Pyridine nucleotide coenzyme specificity of p-hydroxybenzoate hydroxylase and related flavoprotein monooxygenases (2018), Front. Microbiol., 9, 3050 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene pobA, DNA and amino acid sequence determination and analysis and tree, sequence comparisons and phylogenetic analysis, recombinant expression of optimized enzyme, subcloning in Escherichia coli strain DH5alpha Rhodococcus opacus
gene pobA, DNA and amino acid sequence determination and analysis and tree, sequence comparisons and phylogenetic analysis, recombinant expression of optimized enzyme, subcloning in Escherichia coli strain DH5alpha Rhodococcus rhodnii
gene Reut_B5020, DNA sequence comparisons and phylogenetic analysis and tree, recombinant expression of the codon-optimized gene in Acinetobacter sp. ADP1 Cupriavidus pinatubonensis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0194
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination, with NADPH Cupriavidus pinatubonensis
0.0202
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination, with NADH Cupriavidus pinatubonensis
0.0204
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via product determination per HPLC, with NADPH Cupriavidus pinatubonensis
0.0304
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination Rhodococcus opacus
0.035
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination, with NADPH Rhodococcus opacus
0.0397
-
NADH pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination Rhodococcus opacus
0.042
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via product determination per HPLC, with NADPH Rhodococcus opacus
0.0498
-
NADH pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination Cupriavidus pinatubonensis
0.0499
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via product determination per HPLC Rhodococcus opacus
0.146
-
NADPH pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, UV/VIS-NAD(P)H consumption determination Cupriavidus pinatubonensis
0.153
-
NADPH pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, UV/VIS-NAD(P)H consumption determination Rhodococcus opacus
0.193
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via product determination per HPLC, with NADH Cupriavidus pinatubonensis

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4-hydroxybenzoate + NADH + H+ + O2 Cupriavidus pinatubonensis
-
3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2 Rhodococcus rhodnii
-
3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2 Rhodococcus opacus preferred substrates 3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2 Rhodococcus rhodnii 135
-
3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2 Rhodococcus opacus 557 preferred substrates 3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADPH + H+ + O2 Cupriavidus pinatubonensis
-
3,4-dihydroxybenzoate + NADP+ + H2O
-
?
4-hydroxybenzoate + NADPH + H+ + O2 Rhodococcus opacus
-
3,4-dihydroxybenzoate + NADP+ + H2O
-
?
4-hydroxybenzoate + NADPH + H+ + O2 Rhodococcus opacus 557
-
3,4-dihydroxybenzoate + NADP+ + H2O
-
?

Organism

Organism UniProt Comment Textmining
Cupriavidus pinatubonensis Q46R66 Cupriavidus necator or Ralstonia eutropha
-
Rhodococcus opacus A0A0U1URQ7
-
-
Rhodococcus opacus 557 A0A0U1URQ7
-
-
Rhodococcus rhodnii A0A0U1URV4
-
-
Rhodococcus rhodnii 135 A0A0U1URV4
-
-

Source Tissue

Source Tissue Comment Organism Textmining
additional information culture growth with 4-hydroxybenzoate as sole source of carbon and energy Rhodococcus opacus
-
additional information culture growth with 4-hydroxybenzoate as sole source of carbon and energy Rhodococcus rhodnii
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4-hydroxybenzoate + NADH + H+ + O2
-
Cupriavidus pinatubonensis 3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2
-
Rhodococcus rhodnii 3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2 preferred substrates Rhodococcus opacus 3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2
-
Rhodococcus rhodnii 135 3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADH + H+ + O2 preferred substrates Rhodococcus opacus 557 3,4-dihydroxybenzoate + NAD+ + H2O
-
?
4-hydroxybenzoate + NADPH + H+ + O2
-
Cupriavidus pinatubonensis 3,4-dihydroxybenzoate + NADP+ + H2O
-
?
4-hydroxybenzoate + NADPH + H+ + O2
-
Rhodococcus opacus 3,4-dihydroxybenzoate + NADP+ + H2O
-
?
4-hydroxybenzoate + NADPH + H+ + O2
-
Rhodococcus opacus 557 3,4-dihydroxybenzoate + NADP+ + H2O
-
?
additional information enzyme PHBHRo shows a clear preference for NADH compared to NADPH Rhodococcus opacus ?
-
-
additional information enzyme PHBHRr shows a clear preference for NADH compared to NADPH Rhodococcus rhodnii ?
-
-
additional information enzyme PHBHRr shows a clear preference for NADH compared to NADPH Rhodococcus rhodnii 135 ?
-
-
additional information enzyme PHBHRo shows a clear preference for NADH compared to NADPH Rhodococcus opacus 557 ?
-
-

Subunits

Subunits Comment Organism
More PHBH and related enzymes lack a canonical NAD(P)H-binding domain Cupriavidus pinatubonensis
More PHBH and related enzymes lack a canonical NAD(P)H-binding domain Rhodococcus opacus
More PHBH and related enzymes lack a canonical NAD(P)H-binding domain Rhodococcus rhodnii

Synonyms

Synonyms Comment Organism
NAD(P)H-dependent PHBHCn1
-
Cupriavidus pinatubonensis
NADPH-dependent PHBH UniProt Rhodococcus opacus
p-hydroxybenzoate hydroxylase
-
Cupriavidus pinatubonensis
p-hydroxybenzoate hydroxylase
-
Rhodococcus opacus
p-hydroxybenzoate hydroxylase
-
Rhodococcus rhodnii
PHBH
-
Cupriavidus pinatubonensis
PHBH
-
Rhodococcus opacus
PHBH
-
Rhodococcus rhodnii
PHBHCn1
-
Cupriavidus pinatubonensis
PHBHRo
-
Rhodococcus opacus
PHBHRo1CP
-
Rhodococcus opacus
PHBHRr
-
Rhodococcus rhodnii
PobA
-
Rhodococcus opacus
PobA
-
Rhodococcus rhodnii
Reut_B5020
-
Cupriavidus pinatubonensis

Temperature Optimum [┬░C]

Temperature Optimum [┬░C] Temperature Optimum Maximum [┬░C] Comment Organism
30
-
assay at Cupriavidus pinatubonensis
30
-
assay at Rhodococcus opacus
30
-
assay at Rhodococcus rhodnii

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.6
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via product determination per HPLC, with NADPH Cupriavidus pinatubonensis
6.5
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination, with NADPH Cupriavidus pinatubonensis
6.8
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via product determination per HPLC, with NADH Cupriavidus pinatubonensis
7.6
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination, with NADH Cupriavidus pinatubonensis
8.7
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination, with NADPH Rhodococcus opacus
9.4
-
NADH pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination Cupriavidus pinatubonensis
9.6
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via product determination per HPLC, with NADPH Rhodococcus opacus
12.9
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination, with NADH Rhodococcus opacus
15
-
NADPH pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, UV/VIS-NAD(P)H consumption determination Rhodococcus opacus
15.3
-
NADH pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination Rhodococcus opacus
16.8
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via product determination per HPLC, with NADH Rhodococcus opacus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Cupriavidus pinatubonensis
7.5
-
assay at Rhodococcus opacus
7.5
-
assay at Rhodococcus rhodnii

Cofactor

Cofactor Comment Organism Structure
FAD the enzyme is a flavoprotein Cupriavidus pinatubonensis
FAD the enzyme is a flavoprotein Rhodococcus opacus
FAD the enzyme is a flavoprotein Rhodococcus rhodnii
NADH PHBH and related enzymes lack a canonical NAD(P)H-binding domain enzyme PHBHRr shows a clear preference for NADH Rhodococcus rhodnii
NADH PHBH and related enzymes lack a canonical NAD(P)H-binding domain. Enzyme PHBHRo shows a clear preference for NADH, PHBHRo1CP contains the NADH-preferring sequence motif 32-ESRTREEVEGT. NADH is preferred over NADPHs Rhodococcus opacus
NADH PHBH and related enzymes lack a canonical NAD(P)H-binding domain. NAD(P)H-dependent PHBHCn1 Cupriavidus pinatubonensis
NADPH NADH is preferred before NADPH Rhodococcus opacus
NADPH PHBH and related enzymes lack a canonical NAD(P)H-binding domain. NAD(P)H-dependent PHBHCn1 Cupriavidus pinatubonensis

General Information

General Information Comment Organism
evolution amino acid sequences of NADH-preferring PHBHs of putative PHBHs identified in currently available bacterial genomes, phylogenetic analysis, overview. The pyridine nucleotide coenzyme specificity of PHBH emerged through adaptive evolution, and the NADH-preferring enzymes are the older versions of PHBH. Structural comparison and distance tree analysis of group A flavoprotein monooxygenases indicates that a similar protein segment as being responsible for the pyridine nucleotide coenzyme specificity of PHBH is involved in determining the pyridine nucleotide coenzyme specificity of the other group A members. Evolutionary rate calculation. Among the actinobacterial sequences presently available, most comprise the NADH-preferring fingerprint. However, Mycobacteria have a mixed type motif, often the first or both arginine(s) of the NADH-fingerprint are present but the remaining part is lacking. In addition, many mycobacterial sequences have parts of the NADPH-preferring fingerprint, especially, x(D/E)YVL(G/S)R Cupriavidus pinatubonensis
evolution amino acid sequences of NADH-preferring PHBHs of putative PHBHs identified in currently available bacterial genomes, phylogenetic analysis, overview. The pyridine nucleotide coenzyme specificity of PHBH emerged through adaptive evolution, and the NADH-preferring enzymes are the older versions of PHBH. Structural comparison and distance tree analysis of group A flavoprotein monooxygenases indicates that a similar protein segment as being responsible for the pyridine nucleotide coenzyme specificity of PHBH is involved in determining the pyridine nucleotide coenzyme specificity of the other group A members. Evolutionary rate calculation. Among the actinobacterial sequences presently available, most comprise the NADH-preferring fingerprint. However, Mycobacteria have a mixed type motif, often the first or both arginine(s) of the NADH-fingerprint are present but the remaining part is lacking. In addition, many mycobacterial sequences have parts of the NADPH-preferring fingerprint, especially, x(D/E)YVL(G/S)R Rhodococcus opacus
evolution amino acid sequences of NADH-preferring PHBHs of putative PHBHs identified in currently available bacterial genomes, phylogenetic analysis, overview. The pyridine nucleotide coenzyme specificity of PHBH emerged through adaptive evolution, and the NADH-preferring enzymes are the older versions of PHBH. Structural comparison and distance tree analysis of group A flavoprotein monooxygenases indicates that a similar protein segment as being responsible for the pyridine nucleotide coenzyme specificity of PHBH is involved in determining the pyridine nucleotide coenzyme specificity of the other group A members. Evolutionary rate calculation. Among the actinobacterial sequences presently available, most comprise the NADH-preferring fingerprint. However, Mycobacteria have a mixed type motif, often the first or both arginine(s) of the NADH-fingerprint are present but the remaining part is lacking. In addition, many mycobacterial sequences have parts of the NADPH-preferring fingerprint, especially, x(D/E)YVL(G/S)R Rhodococcus rhodnii
additional information energy profiling from enzyme protein structure is realized by means of a coarse-grained residue-level pair potential function modeling, overview Cupriavidus pinatubonensis
additional information energy profiling from enzyme protein structure is realized by means of a coarse-grained residue-level pair potential function modeling, overview Rhodococcus opacus
additional information energy profiling from enzyme protein structure is realized by means of a coarse-grained residue-level pair potential function modeling, overview Rhodococcus rhodnii

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
73.1
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via product determination per HPLC, with NADH Cupriavidus pinatubonensis
98.04
-
NADPH pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, UV/VIS-NAD(P)H consumption determination Rhodococcus opacus
188.8
-
NADH pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination Cupriavidus pinatubonensis
225.5
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via product determination per HPLC, with NADPH Cupriavidus pinatubonensis
228.6
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via product determination per HPLC, with NADPH Rhodococcus opacus
248.6
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination, with NADPH Rhodococcus opacus
335.1
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination, with NADPH Cupriavidus pinatubonensis
336.7
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via product determination per HPLC Rhodococcus opacus
376.2
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHCn1, via UV/VIS-NAD(P)H consumption determination, with NADH Cupriavidus pinatubonensis
385.4
-
NADH pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination Rhodococcus opacus
424.3
-
4-hydroxybenzoate pH 7.5, 30┬░C, recombinant enzyme PHBHRo1CP, via UV/VIS-NAD(P)H consumption determination Rhodococcus opacus