Difference between revisions of "Transformation of LTA4 to LTB4"

From ISMOC
Jump to: navigation, search
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
[[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 14: Line 18:
  
 
== 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 21: Line 26:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 30: Line 36:
 
pH:8
 
pH:8
 
Temperature: 20 (Room Temperature)
 
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>
 
|-
 
|-
Line 39: Line 46:
 
pH:8
 
pH:8
 
Temperature: 20 (Room Temperature)
 
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 48: Line 56:
 
pH: 8
 
pH: 8
 
Temperature:2°C
 
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>
 
|-
 
|-
Line 55: Line 64:
 
pH: 8
 
pH: 8
 
Temperature:37°C
 
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 65: Line 99:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 74: Line 109:
 
pH: 7.4
 
pH: 7.4
 
Temperature: 37 °C
 
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 82: Line 118:
 
Enzyme: Wild Type Leukotriene A4 hydrolase:
 
Enzyme: Wild Type Leukotriene A4 hydrolase:
 
pH:8
 
pH:8
Temperature: 20 (Room Temperature)  
+
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>
 
|-
 
|-
Line 92: Line 129:
 
pH:8
 
pH:8
 
Temperature: 20 (Room Temperature)
 
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 101: Line 139:
 
pH: 8
 
pH: 8
 
Temperature:37°C
 
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"  
 
{|class="wikitable sortable"  
|+  style="text-align: left;" | LTA4H Abundance
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
 
! Value
 
! Value
Line 112: Line 165:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 121: Line 175:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 37 °C
 
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>
 
|<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>
 
|-
 
|-
Line 130: Line 185:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 37 °C
 
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>
 
|<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>
 
|-
 
|-
Line 139: Line 195:
 
pH: 7.5
 
pH: 7.5
 
Temperature: 37 °C
 
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>
 
|<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"  
 
{|class="wikitable sortable"  
|+  style="text-align: left;" | Gibbs Free Energy Change
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
! Value
+
! Gibbs Free Energy Change
 
! Units
 
! Units
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 161: Line 229:
 
pH: 7.3  
 
pH: 7.3  
 
ionic strength: 0.25
 
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>
 
|<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 ==

Latest revision as of 08:39, 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