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Literature summary extracted from

  • Takao, H.; Hirabayashi, K.; Nishigaya, Y.; Kouriki, H.; Nakaniwa, T.; Hagiwara, Y.; Harada, J.; Sato, H.; Yamazaki, T.; Sakakibara, Y.; Suiko, M.; Asada, Y.; Takahashi, Y.; Yamamoto, K.; Fukuyama, K.; Sugishima, M.; Wada, K.
    A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity (2017), Nat. Commun., 8, 14397.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.3.1.24 expressed in Escherichia coli BL21(DE3) cells Rattus norvegicus
1.3.1.24 expressed in Escherichia coli BL21(DE3) cells Homo sapiens
1.3.1.24 expressed in Escherichia coli C41(DE3) cells Synechocystis sp. PCC 6803

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.3.1.24 apo-, NADP+-bound and biliverdin-NADP+ complex forms of the enzyme, hanging drop vapor diffusion method, using 15% (w/v) PEG 4,000, 50 mM Tris-HCl (pH 7.25), 0.2 M sodium acetate and 0.2 mM Cymal-2 Homo sapiens
1.3.1.24 apo-, NADP+-bound and biliverdin-NADP+ complex forms of the enzyme, hanging drop vapor diffusion method, using 15% (w/v) PEG 4,000, 50mM Tris-HCl (pH 7.25), 0.2M sodium acetate and 0.2mM Cymal-2 Rattus norvegicus
1.3.1.24 apo-, NADP+-bound and biliverdin-NADP+ complex forms of the enzyme, hanging drop vapor diffusion method, using 15% (w/v) PEG 4,000, 50mM Tris-HCl (pH 7.25), 0.2M sodium acetate and 0.2mM Cymal-2 Synechocystis sp. PCC 6803

Protein Variants

EC Number Protein Variants Comment Organism
1.3.1.24 K237A the mutant shows increased catalytic efficiency compared to the wild type enzyme Synechocystis sp. PCC 6803
1.3.1.24 R171A the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Rattus norvegicus
1.3.1.24 R171E the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Rattus norvegicus
1.3.1.24 R171K the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Rattus norvegicus
1.3.1.24 R172A the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Homo sapiens
1.3.1.24 R172E inactive Homo sapiens
1.3.1.24 R172K inactive Homo sapiens
1.3.1.24 R185A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Synechocystis sp. PCC 6803
1.3.1.24 R185K the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Synechocystis sp. PCC 6803
1.3.1.24 R188A the mutant shows increased catalytic efficiency compared to the wild type enzyme Synechocystis sp. PCC 6803
1.3.1.24 R246A the mutant shows reduced catalytic efficiency compared to the wild type enzyme Synechocystis sp. PCC 6803
1.3.1.24 S184A the mutant shows increased catalytic efficiency compared to the wild type enzyme Synechocystis sp. PCC 6803
1.3.1.24 T169A the mutant shows wild type catalytic efficiency Synechocystis sp. PCC 6803
1.3.1.24 Y102F the mutant shows reduced catalytic efficiency compared to the wild type enzyme Synechocystis sp. PCC 6803
1.3.1.24 Y97F the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme Rattus norvegicus
1.3.1.24 Y98F the mutant shows about wild type catalytic efficiency Rattus norvegicus
1.3.1.24 Y98F the mutant shows about wild type catalytic efficiency Homo sapiens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.3.1.24 0.0018
-
 Biliverdin wild type enzyme, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0019
-
 Biliverdin mutant enzyme S184A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0033
-
 Biliverdin mutant enzyme R188A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0034
-
 Biliverdin mutant enzyme T169A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0038
-
 Biliverdin mutant enzyme Y98F, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 0.004
-
 Biliverdin mutant enzyme Y102F, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0046
-
 Biliverdin wild type enzyme, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 0.0048
-
 Biliverdin mutant enzyme K237A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0051
-
 Biliverdin mutant enzyme R246A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0069
-
 Biliverdin mutant enzyme R185A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0117
-
 Biliverdin mutant enzyme Y97F, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 0.0126
-
 Biliverdin mutant enzyme R185K, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.0207
-
 Biliverdin wild type enzyme, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 0.0244
-
 Biliverdin mutant enzyme R171A, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 0.0457
-
 Biliverdin mutant enzyme R171E, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 0.0877
-
 Biliverdin mutant enzyme R172A, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 0.1633
-
 Biliverdin mutant enzyme R171K, at pH 8.9, temperature not specified in the publication Rattus norvegicus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.3.1.24 biliverdin + NADH + H+ Rattus norvegicus
-
 bilirubin + NAD+
-
 r
1.3.1.24 biliverdin + NADH + H+ Homo sapiens
-
 bilirubin + NAD+
-
 r
1.3.1.24 biliverdin + NADH + H+ Synechocystis sp. PCC 6803
-
 bilirubin + NAD+
-
 r
1.3.1.24 biliverdin + NADPH + H+ Rattus norvegicus
-
 bilirubin + NADP+
-
 r
1.3.1.24 biliverdin + NADPH + H+ Homo sapiens
-
 bilirubin + NADP+
-
 r
1.3.1.24 biliverdin + NADPH + H+ Synechocystis sp. PCC 6803
-
 bilirubin + NADP+
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.3.1.24 Homo sapiens P53004
-
-
1.3.1.24 Rattus norvegicus P06762
-
-
1.3.1.24 Synechocystis sp. PCC 6803 P72782
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.3.1.24 nickel affinity gel chromatography and Sephacryl S-200 gel filtration Rattus norvegicus
1.3.1.24 nickel affinity gel chromatography and Sephacryl S-200 gel filtration Homo sapiens
1.3.1.24 nickel affinity gel chromatography and Sephacryl S-200 gel filtration Synechocystis sp. PCC 6803

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.3.1.24 biliverdin + NADH + H+
-
 Rattus norvegicus bilirubin + NAD+
-
 r
1.3.1.24 biliverdin + NADH + H+
-
 Homo sapiens bilirubin + NAD+
-
 r
1.3.1.24 biliverdin + NADH + H+
-
 Synechocystis sp. PCC 6803 bilirubin + NAD+
-
 r
1.3.1.24 biliverdin + NADPH + H+
-
 Rattus norvegicus bilirubin + NADP+
-
 r
1.3.1.24 biliverdin + NADPH + H+
-
 Homo sapiens bilirubin + NADP+
-
 r
1.3.1.24 biliverdin + NADPH + H+
-
 Synechocystis sp. PCC 6803 bilirubin + NADP+
-
 r

Synonyms

EC Number Synonyms Comment Organism
1.3.1.24 BVR
-
 Rattus norvegicus
1.3.1.24 BVR
-
 Homo sapiens
1.3.1.24 BVR
-
 Synechocystis sp. PCC 6803

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.3.1.24 0.7
-
 Biliverdin mutant enzyme R171E, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 0.7
-
 Biliverdin mutant enzyme R185A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 0.9
-
 Biliverdin mutant enzyme R185K, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 2 3.7 Biliverdin mutant enzyme K237A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 2.7
-
 Biliverdin mutant enzyme Y102F, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 6
-
 Biliverdin mutant enzyme R171A, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 7.1
-
 Biliverdin wild type enzyme, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 11
-
 Biliverdin mutant enzyme R246A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 11.3
-
 Biliverdin mutant enzyme S184A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 13.1
-
 Biliverdin mutant enzyme T169A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 13.4
-
 Biliverdin mutant enzyme R188A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 13.6
-
 Biliverdin mutant enzyme Y97F, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 14.7
-
 Biliverdin mutant enzyme R171K, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 16.8
-
 Biliverdin mutant enzyme Y98F, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 17.9
-
 Biliverdin mutant enzyme R172A, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 69.3
-
 Biliverdin wild type enzyme, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 94.8
-
 Biliverdin wild type enzyme, at pH 8.9, temperature not specified in the publication Homo sapiens

Cofactor

EC Number Cofactor Comment Organism Structure
1.3.1.24 NADH
-
 Rattus norvegicus
1.3.1.24 NADH
-
 Homo sapiens
1.3.1.24 NADH
-
 Synechocystis sp. PCC 6803
1.3.1.24 NADPH
-
 Rattus norvegicus
1.3.1.24 NADPH
-
 Homo sapiens
1.3.1.24 NADPH
-
 Synechocystis sp. PCC 6803

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.3.1.24 20
-
 Biliverdin mutant enzyme R171E, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 70
-
 Biliverdin mutant enzyme R185K, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 100
-
 Biliverdin mutant enzyme R171K, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 100
-
 Biliverdin mutant enzyme R185A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 200
-
 Biliverdin mutant enzyme R171A, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 200
-
 Biliverdin mutant enzyme R172A, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 700
-
 Biliverdin mutant enzyme Y102F, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 1200
-
 Biliverdin mutant enzyme Y97F, at pH 8.9, temperature not specified in the publication Rattus norvegicus
1.3.1.24 2200
-
 Biliverdin mutant enzyme R246A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 3900
-
 Biliverdin mutant enzyme T169A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 3900
-
 Biliverdin wild type enzyme, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 4100
-
 Biliverdin mutant enzyme R188A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 4400
-
 Biliverdin mutant enzyme Y98F, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 4600
-
 Biliverdin wild type enzyme, at pH 8.9, temperature not specified in the publication Homo sapiens
1.3.1.24 4900
-
 Biliverdin mutant enzyme K237A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 5900
-
 Biliverdin mutant enzyme S184A, at pH 5.8, temperature not specified in the publication Synechocystis sp. PCC 6803
1.3.1.24 15100
-
 Biliverdin wild type enzyme, at pH 8.9, temperature not specified in the publication Rattus norvegicus