Difference between revisions of "Transformation of PGH2 to PGD2"

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== Enzyme Parameters ==
 
== Enzyme Parameters ==
 +
===K<sub>ms</sub>===
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
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|+  style="text-align: left;" | Michaelis-Menten Constants
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|+  style="text-align: left;" | Literature values
 
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|-
 
! Value
 
! Value
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|-
 
|-
 
|}
 
|}
 +
 +
{| 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
 +
|}
 +
 +
===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
 +
|}
 +
 +
===k<sub>cat</sub>===
  
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
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|+  style="text-align: left;" | Enzyme Turnover Numbers
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|+  style="text-align: left;" | Literature values
 
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|-
 
! Value
 
! Value
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|}
 
|}
  
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{| 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
 +
|}
  
−
 
+
=== Enzyme concentrations ===
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
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|+  style="text-align: left;" | PGDS Abundance
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|+  style="text-align: left;" | Literature values
 
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|-
 
! Value
 
! Value
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|}
 
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PGDS concentration distribution
 +
! Mode (mM) !! Confidence Interval !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 6.76E+01 || 1.64E+00 || 4.41E+00 || 4.49E-01
 +
|}
 +
 +
 +
===K<sub>eq</sub>===
 
{|class="wikitable sortable"  
 
{|class="wikitable sortable"  
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|+  style="text-align: left;" | Gibbs Free Energy Change
+
|+  style="text-align: left;" | Literature values
 
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|-
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! Value
+
! Gibbs Free Energy Change
 
! Units
 
! Units
 
! Species
 
! Species
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ionic strength: 0.25
 
ionic strength: 0.25
 
|<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
 
|}
 
|}
  

Revision as of 08:11, 16 May 2019

Return to overview

The isomerisation of PGH2 to PGD2 is performed by PGDS to yield 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 which does not require glutathione for catalysis and H-PGDS, the hemopoietic type which does require glutathione. L-PGDSG is typically found in the brain, heart and testis, whereas H-PGDS is primarily found in the cytoplasm (Zhou2010 ref 6 and 7).

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.

Reaction

R21 PGH2 - PGD2.jpg

Chemical equation

PGH2 \rightleftharpoons PGD2

Rate equation

R21.PNG

Enzyme Parameters

Kms

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

Enzyme: PGDS pH: 8 Temperature: 25

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

Enzyme: PGDS pH:10 Temperature: Unspecified

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

Enzyme: PGDS pH:6.5 Temperature: Unspecified

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

Enzyme: PGDS pH:7 Temperature: 25

[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

Kmp

Description of the PGDS Kmp distribution
Mode (mM) Location parameter (µ) Scale parameter (σ)
1.30E-02 -4.02E+00 5.69E-01

kcat

Literature values
Value Units Species Notes Reference
158.4 per minute Human Expression Vector: Human Cell

Enzyme: PGDS pH: 8 Temperature: 25

[1]
1302 per minute Human Expression Vector: E. Coli.

Enzyme: PGDS pH:6.5 Temperature: Unspecified

[3]
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

Enzyme concentrations

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

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

[5]
101 ppm Human Expression Vector: Oral Cavity

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

[6]
67.9 ppm Human Expression Vector: Esophagus

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

[5]
44.5 ppm Human Expression Vector:Skin

Enzyme: PGDS pH: 7.5 Temperature: 37 °C

[6]
Description of the PGDS concentration distribution
Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
6.76E+01 1.64E+00 4.41E+00 4.49E-01


Keq

Literature values
Gibbs Free Energy Change Units Species Notes Reference
caption kJ/mol Human Expression Vector: E. Coli

Enzyme: L-PGDS pH: 8 Temperature: 25

[7]
5.72 kcal/mol Not stated Estimated

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

[8]
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

References

  1. ↑ 1.0 1.1 [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. ] Cite error: Invalid <ref> tag; name "Zhou2010" defined multiple times with different content
  2. ↑ [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. ]
  3. ↑ 3.0 3.1 [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. ]
  4. ↑ [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.]
  5. ↑ 5.0 5.1 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. ↑ [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]
  8. ↑ 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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