Difference between revisions of "Transformation of LTA4 to LTB4"

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[[Welcome to the In-Silico Model of Cutaneous Lipids Wiki | Return to overview]]
 
[[Welcome to the In-Silico Model of Cutaneous Lipids Wiki | Return to overview]]
 +
 +
LTA4 is subsequently enzymatically hydrolysed to LTB4 by LTA4 hydrolase (LTA4H). The enzyme performs this reaction by opening the epoxide and creating a carbocation intermediate. The charge of the carbocation delocalises over the triene system and is subsequently subject to nucleophilic attack by water at C12, resulting in the stereospecific addition of a hydroxyl group and the generation of LTB4.
 +
 +
 
== Reaction ==
 
== Reaction ==
  
Line 6: Line 10:
 
==Chemical equation==
 
==Chemical equation==
  
−
<center><math> AA \rightleftharpoons PGH2 </math></center>
+
<center><math> LTA4 \rightleftharpoons LTB4 </math></center>
  
 
== Rate equation ==
 
== Rate equation ==
  
 +
 +
[[File:R15.PNG|center|500px]]
  
 
== Parameters ==
 
== Parameters ==
 +
=== K<sub>ms</sub> ===
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
−
|+  style="text-align: left;" | Michaelis-Menten Constants
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
 
! Value
 
! Value
Line 19: Line 26:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 24: Line 32:
 
|mM
 
|mM
 
|Human
 
|Human
−
|Wild Type, pH 8.0, at room temperature.
+
|Expression Vector: E. Coli
 +
Enzyme: Wild Type Leukotriene A4 hydrolase:
 +
pH:8
 +
Temperature: 20 (Room Temperature)
 +
|128
 
|<ref name="Mueller1996"> [www.ncbi.nlm.nih.gov/pubmed/8650196 Mueller M. , "Leukotriene A4 hydrolase: protection from mechanism-based inactivation by mutation of tyrosine-378.'' Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5931-5.]</ref>
 
|<ref name="Mueller1996"> [www.ncbi.nlm.nih.gov/pubmed/8650196 Mueller M. , "Leukotriene A4 hydrolase: protection from mechanism-based inactivation by mutation of tyrosine-378.'' Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5931-5.]</ref>
 
|-
 
|-
 
|2.70E-03
 
|2.70E-03
 
|mM
 
|mM
−
|Human
+
|Frog
−
|Leukocytes, pH 8.0 at room temperature.
+
|Expression Vector: oocytes
 +
Enzyme: leukotriene  A4  hydrolase
 +
pH:8
 +
Temperature: 20 (Room Temperature)
 +
|16
 
|<ref name="Stromberg1998"> [www.ncbi.nlm.nih.gov/pubmed/9744798 Stromberg F. , "Purification and characterization of leukotriene A4 hydrolase from Xenopus laevis oocytes.'' FEBS Lett. 1998 Aug 21;433(3):219-22.]</ref>
 
|<ref name="Stromberg1998"> [www.ncbi.nlm.nih.gov/pubmed/9744798 Stromberg F. , "Purification and characterization of leukotriene A4 hydrolase from Xenopus laevis oocytes.'' FEBS Lett. 1998 Aug 21;433(3):219-22.]</ref>
 
|-
 
|-
Line 36: Line 52:
 
|rowspan=2|mM
 
|rowspan=2|mM
 
|rowspan=2|Human
 
|rowspan=2|Human
−
|2°C, pH 8.0
+
|Expression Vector: Leukocytes
 +
Enzyme: Leukotriene A4 Hydrolase
 +
pH: 8
 +
Temperature:2°C
 +
|256
 
|rowspan=2|<ref name="Radmark1984"> [www.ncbi.nlm.nih.gov/pubmed/6490615 Radmark O. , "Leukotriene A4 hydrolase in human leukocytes. Purification and properties'' J Biol Chem. 1984 Oct 25;259(20):12339-45.]</ref>
 
|rowspan=2|<ref name="Radmark1984"> [www.ncbi.nlm.nih.gov/pubmed/6490615 Radmark O. , "Leukotriene A4 hydrolase in human leukocytes. Purification and properties'' J Biol Chem. 1984 Oct 25;259(20):12339-45.]</ref>
 
|-
 
|-
 
|2.30E-03
 
|2.30E-03
−
|37°C, pH 8.0
+
|Expression Vector: Leukocytes
 +
Enzyme: Leukotriene A4 Hydrolase
 +
pH: 8
 +
Temperature:37°C
 +
|1024
 +
|
 +
|-
 +
|}
 +
 
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the LTA4H Kms distribution
 +
! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 
|-
 
|-
 +
| 2.40E-03 || 5.77E+00 || -5.51E+00 || 7.20E-01
 
|}
 
|}
  
 +
[[Image:49.jpg|none|thumb|500px|The estimated probability distribution for LTA4H Kms. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.  ]]
 +
 +
 +
===K<sub>mp</sub>===
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the LTA4H Kmp distribution
 +
! Mode (mM) !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 2.40E-03 || -5.51E+00 || 7.17E-01
 +
|}
 +
 +
[[Image:50.jpg|none|thumb|500px|The estimated probability distribution for LTA4H Kmp. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.  ]]
 +
 +
 +
===k<sub>cat</sub>===
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
−
|+  style="text-align: left;" | Enzyme Turnover Numbers
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
 
! Value
 
! Value
Line 51: Line 99:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 56: Line 105:
 
|per minute
 
|per minute
 
|Human
 
|Human
−
|Wild type enzyme, pH 7.4, 37 °C.
+
|Expression Vector: E. Coli.
 +
Enzyme: Leukotriene A4 Hydrolase
 +
pH: 7.4
 +
Temperature: 37 °C
 +
|1024
 
|<ref name="Rudberg2002"> [www.ncbi.nlm.nih.gov/pubmed/11675384 Rudberg P. , "Leukotriene A4 Hydrolase/Aminopeptidase'' The Journal of Biological Chemistry, 277, 1398-1404.]</ref>  
 
|<ref name="Rudberg2002"> [www.ncbi.nlm.nih.gov/pubmed/11675384 Rudberg P. , "Leukotriene A4 Hydrolase/Aminopeptidase'' The Journal of Biological Chemistry, 277, 1398-1404.]</ref>  
 
|-
 
|-
Line 62: Line 115:
 
|per minute
 
|per minute
 
|Human
 
|Human
−
|Wild Type, pH 8.0, at room temperature.
+
|Expression Vector: E. Coli
 +
Enzyme: Wild Type Leukotriene A4 hydrolase:
 +
pH:8
 +
Temperature: 20 (Room Temperature)
 +
|128
 
|<ref name="Mueller1996"> [www.ncbi.nlm.nih.gov/pubmed/8650196 Mueller M. , "Leukotriene A4 hydrolase: protection from mechanism-based inactivation by mutation of tyrosine-378.'' Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5931-5.]</ref>
 
|<ref name="Mueller1996"> [www.ncbi.nlm.nih.gov/pubmed/8650196 Mueller M. , "Leukotriene A4 hydrolase: protection from mechanism-based inactivation by mutation of tyrosine-378.'' Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5931-5.]</ref>
 
|-
 
|-
 
|90
 
|90
 
|per minute
 
|per minute
−
|Human
+
|Frog
−
|Leukocytes, pH 8.0 at room temperature.
+
|Expression Vector: oocytes
 +
Enzyme: leukotriene  A4  hydrolase
 +
pH:8
 +
Temperature: 20 (Room Temperature)
 +
|16
 
|<ref name="Stromberg1998"> [www.ncbi.nlm.nih.gov/pubmed/9744798 Stromberg F. , "Purification and characterization of leukotriene A4 hydrolase from Xenopus laevis oocytes.'' FEBS Lett. 1998 Aug 21;433(3):219-22.]</ref>
 
|<ref name="Stromberg1998"> [www.ncbi.nlm.nih.gov/pubmed/9744798 Stromberg F. , "Purification and characterization of leukotriene A4 hydrolase from Xenopus laevis oocytes.'' FEBS Lett. 1998 Aug 21;433(3):219-22.]</ref>
 
|-
 
|-
Line 74: Line 135:
 
|per minute
 
|per minute
 
|Human
 
|Human
−
|Leukcyte pH 8.0, 37 °C
+
|Expression Vector: Leukocytes
 +
Enzyme: Leukotriene A4 Hydrolase
 +
pH: 8
 +
Temperature:37°C
 +
|1024
 
|<ref name="Radmark1984"> [www.ncbi.nlm.nih.gov/pubmed/6490615 Radmark O. , "Leukotriene A4 hydrolase in human leukocytes. Purification and properties'' J Biol Chem. 1984 Oct 25;259(20):12339-45.]</ref>
 
|<ref name="Radmark1984"> [www.ncbi.nlm.nih.gov/pubmed/6490615 Radmark O. , "Leukotriene A4 hydrolase in human leukocytes. Purification and properties'' J Biol Chem. 1984 Oct 25;259(20):12339-45.]</ref>
 
|-
 
|-
 
|}
 
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the LTA4H kcat distribution
 +
! Mode (min-1) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 2.85E+01 || 6.56E+00 || 3.94E+00 || 7.60E-01
 +
|}
 +
 +
[[Image:51.jpg|none|thumb|500px|The estimated probability distribution for LTA4H kcat. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.  ]]
 +
 +
 +
===Enzyme concentration===
 +
 +
To convert the enzyme concentration from ppm to mM, the following [[Common equations#Enzyme concentration (mM)|equation]] was used.
 +
 +
{|class="wikitable sortable"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 +
! Value
 +
! Units
 +
! Species
 +
! Notes
 +
! Weight
 +
! Reference
 +
|-
 +
|714
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Lung
 +
Enzyme: LTA4H
 +
pH: 7.5
 +
Temperature: 37 °C
 +
|1024
 +
|<ref name="Kim2014"> [http://www.nature.com/nature/journal/v509/n7502/pdf/nature13302.pdf M. Kim ''A draft map of the human proteome'' Nature, 2014 509, 575–581]</ref>
 +
|-
 +
|489
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Skin
 +
Enzyme: LTA4H
 +
pH: 7.5
 +
Temperature: 37 °C
 +
|2048
 +
|<ref name="Wilhelm2014"> [http://www.nature.com/nature/journal/v509/n7502/pdf/nature13319.pdf M. Wilhelm ''Mass-spectrometry-based draft of the human proteome'' Nature, 2014 509, 582–587]</ref>
 +
|-
 +
|410
 +
|<math> ppm </math>
 +
|Human
 +
|Expression Vector: Oral Cavity
 +
Enzyme: LTA4H
 +
pH: 7.5
 +
Temperature: 37 °C
 +
|1024
 +
|<ref name="Wilhelm2014"> [http://www.nature.com/nature/journal/v509/n7502/pdf/nature13319.pdf M. Wilhelm ''Mass-spectrometry-based draft of the human proteome'' Nature, 2014 509, 582–587]</ref>
 +
|-
 +
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the LTA4H concentration distribution
 +
! Mode (ppm) !! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 4.88E+02 ||2.70E-03|| 1.25E+00 || 6.24E+00 || 2.19E-01
 +
|}
 +
 +
[[Image:lta4h.jpg|none|thumb|500px|The estimated probability distribution for LTA4H concentration. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.  ]]
 +
 +
===K<sub>eq</sub>===
 +
{|class="wikitable sortable"
 +
|+  style="text-align: left;" | Literature values
 +
|-
 +
! Gibbs Free Energy Change
 +
! Units
 +
! Species
 +
! Notes
 +
! Weight
 +
! Reference
 +
|-
 +
|(-3.6329994)
 +
|kcal/mol
 +
|Not stated
 +
|Estimated
 +
Enzyme: LTA4H
 +
Substrate: LTA4
 +
Product: LTB4
 +
pH: 7.3
 +
ionic strength: 0.25
 +
|64
 +
|<ref name="MetaCyc”>[http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=LEUKOTRIENE-A4-HYDROLASE-RXN Caspi et al 2014, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases," Nucleic Acids Research 42:D459-D471]</ref>
 +
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the LTA4H Keq distribution
 +
! Mode !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 4.64E+02 || 1.00E+01 || 6.93E+00 || 8.90E-01
 +
|}
 +
 +
[[Image:52.jpg|none|thumb|500px|The estimated probability distribution for LTA4H Keq. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.  ]]
 +
 +
== References ==
 +
<references/>
  
 
== Related Reactions ==
 
== Related Reactions ==

Latest revision as of 09:39, 21 August 2019

Return to overview

LTA4 is subsequently enzymatically hydrolysed to LTB4 by LTA4 hydrolase (LTA4H). The enzyme performs this reaction by opening the epoxide and creating a carbocation intermediate. The charge of the carbocation delocalises over the triene system and is subsequently subject to nucleophilic attack by water at C12, resulting in the stereospecific addition of a hydroxyl group and the generation of LTB4.


Reaction

R15 LTA4 - LTB4.jpg

Chemical equation

LTA4 \rightleftharpoons LTB4

Rate equation

R15.PNG

Parameters

Kms

Literature values
Value Units Species Notes Weight Reference
5.80E-03 mM Human Expression Vector: E. Coli

Enzyme: Wild Type Leukotriene A4 hydrolase: pH:8 Temperature: 20 (Room Temperature)

128 [1]
2.70E-03 mM Frog Expression Vector: oocytes

Enzyme: leukotriene A4 hydrolase pH:8 Temperature: 20 (Room Temperature)

16 [2]
2.20E-02 mM Human Expression Vector: Leukocytes

Enzyme: Leukotriene A4 Hydrolase pH: 8 Temperature:2°C

256 [3]
2.30E-03 Expression Vector: Leukocytes

Enzyme: Leukotriene A4 Hydrolase pH: 8 Temperature:37°C

1024
Description of the LTA4H Kms distribution
Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
2.40E-03 5.77E+00 -5.51E+00 7.20E-01
The estimated probability distribution for LTA4H Kms. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.


Kmp

Description of the LTA4H Kmp distribution
Mode (mM) Location parameter (µ) Scale parameter (σ)
2.40E-03 -5.51E+00 7.17E-01
The estimated probability distribution for LTA4H Kmp. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.


kcat

Literature values
Value Units Species Notes Weight Reference
12.6 - 28.2 per minute Human Expression Vector: E. Coli.

Enzyme: Leukotriene A4 Hydrolase pH: 7.4 Temperature: 37 °C

1024 [4]
51 per minute Human Expression Vector: E. Coli

Enzyme: Wild Type Leukotriene A4 hydrolase: pH:8 Temperature: 20 (Room Temperature)

128 [1]
90 per minute Frog Expression Vector: oocytes

Enzyme: leukotriene A4 hydrolase pH:8 Temperature: 20 (Room Temperature)

16 [2]
125 per minute Human Expression Vector: Leukocytes

Enzyme: Leukotriene A4 Hydrolase pH: 8 Temperature:37°C

1024 [3]
Description of the LTA4H kcat distribution
Mode (min-1) Confidence Interval Location parameter (µ) Scale parameter (σ)
2.85E+01 6.56E+00 3.94E+00 7.60E-01
The estimated probability distribution for LTA4H kcat. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.


Enzyme concentration

To convert the enzyme concentration from ppm to mM, the following equation was used.

Literature values
Value Units Species Notes Weight Reference
714 ppm Human Expression Vector: Lung

Enzyme: LTA4H pH: 7.5 Temperature: 37 °C

1024 [5]
489 ppm Human Expression Vector: Skin

Enzyme: LTA4H pH: 7.5 Temperature: 37 °C

2048 [6]
410 ppm Human Expression Vector: Oral Cavity

Enzyme: LTA4H pH: 7.5 Temperature: 37 °C

1024 [6]
Description of the LTA4H concentration distribution
Mode (ppm) Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
4.88E+02 2.70E-03 1.25E+00 6.24E+00 2.19E-01
The estimated probability distribution for LTA4H concentration. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.

Keq

Literature values
Gibbs Free Energy Change Units Species Notes Weight Reference
(-3.6329994) kcal/mol Not stated Estimated

Enzyme: LTA4H Substrate: LTA4 Product: LTB4 pH: 7.3 ionic strength: 0.25

64 [7]
Description of the LTA4H Keq distribution
Mode Confidence Interval Location parameter (µ) Scale parameter (σ)
4.64E+02 1.00E+01 6.93E+00 8.90E-01
The estimated probability distribution for LTA4H Keq. The value and weight of the literature values used to define the distribution are indicated by an orange dashed line. The x axis is plotted on a log-scale.

References

  1. ↑ 1.0 1.1 [www.ncbi.nlm.nih.gov/pubmed/8650196 Mueller M. , "Leukotriene A4 hydrolase: protection from mechanism-based inactivation by mutation of tyrosine-378. Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5931-5.]
  2. ↑ 2.0 2.1 [www.ncbi.nlm.nih.gov/pubmed/9744798 Stromberg F. , "Purification and characterization of leukotriene A4 hydrolase from Xenopus laevis oocytes. FEBS Lett. 1998 Aug 21;433(3):219-22.]
  3. ↑ 3.0 3.1 [www.ncbi.nlm.nih.gov/pubmed/6490615 Radmark O. , "Leukotriene A4 hydrolase in human leukocytes. Purification and properties J Biol Chem. 1984 Oct 25;259(20):12339-45.]
  4. ↑ [www.ncbi.nlm.nih.gov/pubmed/11675384 Rudberg P. , "Leukotriene A4 Hydrolase/Aminopeptidase The Journal of Biological Chemistry, 277, 1398-1404.]
  5. ↑ M. Kim A draft map of the human proteome Nature, 2014 509, 575–581
  6. ↑ 6.0 6.1 M. Wilhelm Mass-spectrometry-based draft of the human proteome Nature, 2014 509, 582–587
  7. ↑ Caspi et al 2014, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases," Nucleic Acids Research 42:D459-D471

Related Reactions

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