Difference between revisions of "Transformation of PGH2 to PGD2"

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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]]
  
−
PGD2 is synthesised from PGH2 via the prostaglandin D synthase (PGDS) enzyme. Upon binding to the D prostanoid (DP) receptor, the prostanoid stimulates keratinocyte cells to produce peptides which target invading pathogens (Homey, Steinhoff et al. 2006). However this species is primarily produced by LCs, mast cells and melanocytes in the cutaneous compartment (Ujihara, Horiguchi et al. 1988, Shimura, Satoh et al. 2010), and as a consequence it is unlikely to be observed in the early experimental procedures of this project.  
+
The isomerisation of PGH2 to PGD2 can be performed by prostaglandin D synthase (PGDS) and prostaglandin F synthase (PGFS). PGDS yields a hydroxyl group at C9 and a ketone group at C11. Two isoforms of PGDS have been found in humans, the lipocalin isoform, L-PGDS, does not require glutathione for catalysis whereas the hemopoietic type, H-PGDS, does require glutathione.
  
 
== Reaction ==
 
== Reaction ==
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==Chemical equation==
 
==Chemical equation==
  
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<center><math> FA \rightleftharpoons AA </math></center>
+
<center><math> PGH2 \rightleftharpoons PGD2 </math></center>
  
 
== Rate equation ==
 
== Rate equation ==
  
 +
[[File:R21.PNG|center|500px]]
  
 
== Enzyme Parameters ==
 
== Enzyme 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 23:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
−
|4.00E-03
+
|0.0138
 
|<math> mM </math>
 
|<math> mM </math>
 
|Human  
 
|Human  
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pH: 8
 
pH: 8
 
Temperature: 25
 
Temperature: 25
−
|<ref name="Zhou2010"> [http://www.ncbi.nlm.nih.gov/pubmed/20667974 Zhou Y. , "Structure-function analysis of human l-prostaglandin D synthase bound with fatty acid molecules.'' FASEB J. 2010 Dec;24(12):4668-77. doi: 10.1096/fj.10-164863. Epub 2010 Jul 28.
+
|512
−
]</ref>
+
|<ref>[http://www.ncbi.nlm.nih.gov/pubmed/20667974 Zhou Y. , "Structure-function analysis of human l-prostaglandin D synthase bound with fatty acid molecules." FASEB J. 2010 Dec;24(12):4668-77. doi: 10.1096/fj.10-164863. Epub 2010 Jul 28.]</ref>
 
|-
 
|-
 
|4.00E-03
 
|4.00E-03
Line 40: Line 43:
 
pH:10
 
pH:10
 
Temperature: Unspecified
 
Temperature: Unspecified
−
+
|256
−
|<ref name="Watanabe1994"> [http://www.ncbi.nlm.nih.gov/pubmed/8093029 Watanabe K. , "Identification of beta-trace as prostaglandin D synthase.''
+
|<ref>[http://www.ncbi.nlm.nih.gov/pubmed/8093029 Watanabe K. , "Identification of beta-trace as prostaglandin D synthase."Biochem Biophys Res Commun. 1994 Sep 15;203(2):1110-6. ]</ref> 
−
Biochem Biophys Res Commun. 1994 Sep 15;203(2):1110-6. ]</ref>   
+
|-
 +
|0.50
 +
|<math> mM </math>
 +
|Human
 +
|Expression Vector: E. Coli.
 +
Enzyme: PGDS
 +
pH:6.5
 +
Temperature: Unspecified
 +
|128
 +
|<ref>[https://www.ncbi.nlm.nih.gov/pubmed/10871602 Pinzar E , "Structural basis of hematopoietic prostaglandin D synthase activity elucidated by site-directed mutagenesis." J Biol Chem. 2000 Oct 6;275(40):31239-44. ]</ref>
 +
|-
 +
|1.40E-02
 +
|<math> mM </math>
 +
|Rat
 +
|Expression Vector: Cerebrospinal Fluid
 +
Enzyme: PGDS
 +
pH:7
 +
Temperature: 25
 +
|256
 +
|<ref>[https://www.ncbi.nlm.nih.gov/pubmed/3930495 Urade Y. , "Purification and characterization of rat brain prostaglandin D synthetase." J Biol Chem. 1985 Oct 15;260(23):12410-5.]</ref>   
 
|-
 
|-
 +
|}
 +
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PGDS Kms distribution
 +
! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 1.35E-02 || 3.78E+00 || -3.44E+00 || 9.29E-01
 +
|}
 +
 +
[[Image:65.jpg|none|thumb|500px|The estimated probability distribution for PGDS 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 PGDS Kmp distribution
 +
! Mode (mM) !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 1.30E-02 || -4.02E+00 || 5.69E-01
 
|}
 
|}
 +
 +
[[Image:66.jpg|none|thumb|500px|The estimated probability distribution for PGDS 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 54: Line 97:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 63: Line 107:
 
pH: 8
 
pH: 8
 
Temperature: 25
 
Temperature: 25
 +
|256
 
| <ref name="Zhou2010"> [http://www.ncbi.nlm.nih.gov/pubmed/20667974 Zhou Y. , "Structure-function analysis of human l-prostaglandin D synthase bound with fatty acid molecules.'' FASEB J. 2010 Dec;24(12):4668-77.]</ref>  
 
| <ref name="Zhou2010"> [http://www.ncbi.nlm.nih.gov/pubmed/20667974 Zhou Y. , "Structure-function analysis of human l-prostaglandin D synthase bound with fatty acid molecules.'' FASEB J. 2010 Dec;24(12):4668-77.]</ref>  
 +
|-
 +
|1302
 +
| per minute
 +
|Human
 +
|Expression Vector: E. Coli.
 +
Enzyme: PGDS
 +
pH:6.5
 +
Temperature: Unspecified
 +
|128
 +
|<ref name="Pinzar2000"> [https://www.ncbi.nlm.nih.gov/pubmed/10871602 Pinzar E , "Structural basis of hematopoietic prostaglandin D synthase activity elucidated by site-directed mutagenesis.''
 +
J Biol Chem. 2000 Oct 6;275(40):31239-44. ]</ref>
 +
|-
 
|}
 
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PGDS kcat distribution
 +
! Mode (min-1) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 1.58E+02 || 1.50E+00 || 5.10E+00 || 2.00E-01
 +
|}
 +
 +
[[Image:67.jpg|none|thumb|500px|The estimated probability distribution for PGDS 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 concentrations ===
  
 +
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;" | PGDS Abundance
+
|+  style="text-align: left;" | Literature values
 
|-
 
|-
 
! Value
 
! Value
Line 75: Line 144:
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 84: Line 154:
 
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 93: Line 164:
 
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>
 
|-
 
|-
Line 102: Line 174:
 
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 111: Line 184:
 
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>
 
|-
 
|-
 
|}
 
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PGDS concentration distribution
 +
! Mode (ppm) !! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 6.76E+01 ||3.74E-04|| 1.64E+00 || 4.41E+00 || 4.49E-01
 +
|}
 +
 +
[[Image:161.jpg|none|thumb|500px|The estimated probability distribution for PGDS 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 131: Line 216:
 
pH: 8
 
pH: 8
 
Temperature: 25
 
Temperature: 25
 +
|64
 
|<ref name="Kume2014"> [http://ac.els-cdn.com/S0014579314000982/1-s2.0-S0014579314000982-main.pdf?_tid=7f323a24-6543-11e6-82ac-00000aab0f01&acdnat=1471525305_289e200c1e492c5fa693179a5396fd82 Kume S., "Fine-tuned broad binding capability of human lipocalin-type prostaglandin D synthase for various small lipophilic ligands'' FEBS Letters
 
|<ref name="Kume2014"> [http://ac.els-cdn.com/S0014579314000982/1-s2.0-S0014579314000982-main.pdf?_tid=7f323a24-6543-11e6-82ac-00000aab0f01&acdnat=1471525305_289e200c1e492c5fa693179a5396fd82 Kume S., "Fine-tuned broad binding capability of human lipocalin-type prostaglandin D synthase for various small lipophilic ligands'' FEBS Letters
 
Volume 588, Issue 6, 18 March 2014, Pages 962–969]</ref>
 
Volume 588, Issue 6, 18 March 2014, Pages 962–969]</ref>
Line 143: 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=PROSTAGLANDIN-D-SYNTHASE-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=PROSTAGLANDIN-D-SYNTHASE-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 PGDS Keq distribution
 +
! Mode !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 7.46E+04 || 1.00E+01 || 1.20E+01 || 8.90E-01
 +
|}
 +
 +
[[Image:68.jpg|none|thumb|500px|The estimated probability distribution for PGDS 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 08:51, 21 August 2019

Return to overview

The isomerisation of PGH2 to PGD2 can be performed by prostaglandin D synthase (PGDS) and prostaglandin F synthase (PGFS). PGDS yields a hydroxyl group at C9 and a ketone group at C11. Two isoforms of PGDS have been found in humans, the lipocalin isoform, L-PGDS, does not require glutathione for catalysis whereas the hemopoietic type, H-PGDS, does require glutathione.

Reaction

R21 PGH2 - PGD2.jpg

Chemical equation

PGH2 \rightleftharpoons PGD2

Rate equation

R21.PNG

Enzyme Parameters

Kms

Literature values
Value Units Species Notes Weight Reference
0.0138 mM Human Expression Vector: Human Cell

Enzyme: PGDS pH: 8 Temperature: 25

512 [1]
4.00E-03 mM Human Expression Vector: Cerebrospinal Fluid

Enzyme: PGDS pH:10 Temperature: Unspecified

256 [2]
0.50 mM Human Expression Vector: E. Coli.

Enzyme: PGDS pH:6.5 Temperature: Unspecified

128 [3]
1.40E-02 mM Rat Expression Vector: Cerebrospinal Fluid

Enzyme: PGDS pH:7 Temperature: 25

256 [4]
Description of the PGDS Kms distribution
Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
1.35E-02 3.78E+00 -3.44E+00 9.29E-01
The estimated probability distribution for PGDS 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 PGDS Kmp distribution
Mode (mM) Location parameter (µ) Scale parameter (σ)
1.30E-02 -4.02E+00 5.69E-01
The estimated probability distribution for PGDS 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
158.4 per minute Human Expression Vector: Human Cell

Enzyme: PGDS pH: 8 Temperature: 25

256 [5]
1302 per minute Human Expression Vector: E. Coli.

Enzyme: PGDS pH:6.5 Temperature: Unspecified

128 [6]
Description of the PGDS kcat distribution
Mode (min-1) Confidence Interval Location parameter (µ) Scale parameter (σ)
1.58E+02 1.50E+00 5.10E+00 2.00E-01
The estimated probability distribution for PGDS 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 concentrations

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

Literature values
Value Units Species Notes Weight Reference
156 ppm Human Expression Vector: Pancreas

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

1024 [7]
101 ppm Human Expression Vector: Oral Cavity

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

1024 [8]
67.9 ppm Human Expression Vector: Esophagus

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

1024 [7]
44.5 ppm Human Expression Vector:Skin

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

2048 [8]
Description of the PGDS concentration distribution
Mode (ppm) Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
6.76E+01 3.74E-04 1.64E+00 4.41E+00 4.49E-01
The estimated probability distribution for PGDS 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
caption kJ/mol Human Expression Vector: E. Coli

Enzyme: L-PGDS pH: 8 Temperature: 25

64 [9]
5.72 kcal/mol Not stated Estimated

Enzyme: PGDS Substrate: Arachidonate Product: PGD2 pH: 7.3 ionic strength: 0.25

64 [10]
Description of the PGDS Keq distribution
Mode Confidence Interval Location parameter (µ) Scale parameter (σ)
7.46E+04 1.00E+01 1.20E+01 8.90E-01
The estimated probability distribution for PGDS 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. ↑ Zhou Y. , "Structure-function analysis of human l-prostaglandin D synthase bound with fatty acid molecules." FASEB J. 2010 Dec;24(12):4668-77. doi: 10.1096/fj.10-164863. Epub 2010 Jul 28.
  2. ↑ Watanabe K. , "Identification of beta-trace as prostaglandin D synthase."Biochem Biophys Res Commun. 1994 Sep 15;203(2):1110-6.
  3. ↑ Pinzar E , "Structural basis of hematopoietic prostaglandin D synthase activity elucidated by site-directed mutagenesis." J Biol Chem. 2000 Oct 6;275(40):31239-44.
  4. ↑ Urade Y. , "Purification and characterization of rat brain prostaglandin D synthetase." J Biol Chem. 1985 Oct 15;260(23):12410-5.
  5. ↑ Zhou Y. , "Structure-function analysis of human l-prostaglandin D synthase bound with fatty acid molecules. FASEB J. 2010 Dec;24(12):4668-77.
  6. ↑ [https://www.ncbi.nlm.nih.gov/pubmed/10871602 Pinzar E , "Structural basis of hematopoietic prostaglandin D synthase activity elucidated by site-directed mutagenesis. J Biol Chem. 2000 Oct 6;275(40):31239-44. ]
  7. ↑ 7.0 7.1 M. Kim A draft map of the human proteome Nature, 2014 509, 575–581
  8. ↑ 8.0 8.1 M. Wilhelm Mass-spectrometry-based draft of the human proteome Nature, 2014 509, 582–587
  9. ↑ [http://ac.els-cdn.com/S0014579314000982/1-s2.0-S0014579314000982-main.pdf?_tid=7f323a24-6543-11e6-82ac-00000aab0f01&acdnat=1471525305_289e200c1e492c5fa693179a5396fd82 Kume S., "Fine-tuned broad binding capability of human lipocalin-type prostaglandin D synthase for various small lipophilic ligands FEBS Letters Volume 588, Issue 6, 18 March 2014, Pages 962–969]
  10. ↑ 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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