Difference between revisions of "Transformation of 15-Keto-PGE2 to 13,14-Dihydro-15-Keto-PGE2"

From ISMOC
Jump to: navigation, search
(→‎Parameters)
(→‎Parameters)
 
(15 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]]
  
−
 
+
The second step of the catabolic pathway of prostanoids is the reduction of the conjugated α, β-unsaturated double bond at C13, by 13, 15-ketoprostglandin reductase, also known as prostaglandin reductase. There are two isoforms of this protein, prostaglandin reductase 1 (PTGR-1) and prostaglandin reductase 2 (PTGR-2). Prostaglandin reductase 1 (PTGR-1) can accept a wide variety of prostaglandins as substrates. Prostaglandin reductase 2 (PTGR-2) has the highest affinity for 15-keto-PGE2, but also accepts a wide variety of prostaglandins as a substrate <ref>Wu, Yu-Hauh Ko, Tzu-Ping Guo, Rey-Ting Hu, Su-Ming Chuang, Lee-Ming Wang, Andrew H J., ''Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2'',Structure (2008), 16, 1714-1723.</ref>.
  
 
== Reaction ==
 
== Reaction ==
Line 10: Line 10:
  
 
== Rate equation ==
 
== Rate equation ==
−
 
+
[[File:R69.PNG|center|500px]]
  
 
== Parameters ==
 
== Parameters ==
−
 
+
===K<sub>ms</sub>===
  
 
{|class="wikitable"  
 
{|class="wikitable"  
−
|+  style="text-align: left;" | Michaelis-Menten Constants
+
|+  style="text-align: left;" | Literature values
 
! Value
 
! Value
 
! Units
 
! Units
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 37: Line 38:
 
NADPH, 15-keto-PGE2 at a final concentration of 200 mM was used with different
 
NADPH, 15-keto-PGE2 at a final concentration of 200 mM was used with different
 
concentrations of NADPH (0–60 mM)."
 
concentrations of NADPH (0–60 mM)."
−
 
+
|512
−
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2, Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>  
+
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 "Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2", Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>  
 
|-
 
|-
 
|0.01587 ± 0.00171
 
|0.01587 ± 0.00171
Line 54: Line 55:
 
NADPH, 15-keto-PGE2 at a final concentration of 200 mM was used with different
 
NADPH, 15-keto-PGE2 at a final concentration of 200 mM was used with different
 
concentrations of NADPH (0–60 mM)."
 
concentrations of NADPH (0–60 mM)."
 +
|512
 +
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 "Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2", Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>
 +
|-
 +
|}
 +
  
−
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2, Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>
+
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PTGR-2 Kms distribution
 +
! Mode (mM) !! Confidence Interval  !! Location parameter (µ) !! Scale parameter (σ)
 
|-
 
|-
 +
| 1.20E-02 || 4.92E+00 || -3.97E+00 || 6.71E-01
 +
|}
 +
 +
[[Image:77.jpg|none|thumb|500px|The estimated probability distribution for PTGR-2 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 PTGR-2 Kmp distribution
 +
! Mode (mM) !! Location parameter (µ) !! Scale parameter (σ)
 
|-
 
|-
−
|0.0496 ± 0.0058
+
| 1.19E-02 || -3.97E+00 || 6.81E-01
−
|mM
 
−
| Mouse
 
−
|Method: In vitro
 
−
Organism: Mouse
 
−
Expression vector:
 
−
Enzyme: 13,14-dehydro-15-oxoprostaglandin 13-reductase
 
−
pH: 7.4
 
−
Temperature:  37 ◦C
 
−
Substrate: 15-Ketoprostaglandin E2
 
−
| <ref name="Wu2008"> [http://www.jbc.org/content/282/25/18162.long Identification of a Novel Prostaglandin Reductase Reveals the Involvement of Prostaglandin E2 Catabolism in Regulation of Peroxisome Proliferator-activated Receptor γ Activation, June 22, 2007, The Journal of Biological Chemistry, 282, 18162-18172]</ref>
 
 
|-
 
|-
 +
|
 
|}
 
|}
  
 +
[[Image:78.jpg|none|thumb|500px|The estimated probability distribution for PTGR-2 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>===
 
Note: Turnover values from EC 1.3.1.48 - 13,14-dehydro-15-oxoprostaglandin 13-reductase
 
Note: Turnover values from EC 1.3.1.48 - 13,14-dehydro-15-oxoprostaglandin 13-reductase
  
 
{|class="wikitable"  
 
{|class="wikitable"  
−
|+  style="text-align: left;" | Enzyme Turnover Number
+
|+  style="text-align: left;" | Literature values
 
! Value
 
! Value
 
! Units
 
! Units
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 92: Line 104:
 
Temperature:  37 ◦C
 
Temperature:  37 ◦C
 
Substrate: 15-Ketoprostaglandin E2
 
Substrate: 15-Ketoprostaglandin E2
−
| <ref name="Wu2008"> [http://www.jbc.org/content/282/25/18162.long Identification of a Novel Prostaglandin Reductase Reveals the Involvement of Prostaglandin E2 Catabolism in Regulation of Peroxisome Proliferator-activated Receptor γ Activation, June 22, 2007, The Journal of Biological Chemistry, 282, 18162-18172]</ref>  
+
|384
 +
|<ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 "Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2", Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>  
 
|-
 
|-
 +
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PTGR-2 kcat distribution
 +
! Mode (min-1) !! Confidence Interval  !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 1.14E+01 || 9.86E+00 || 3.22E+00 || 8.87E-01
 
|}
 
|}
  
 +
[[Image:79.jpg|none|thumb|500px|The estimated probability distribution for PTGR-2 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"  
 
{|class="wikitable"  
−
|+  style="text-align: left;" | 5-HEDH Abundance
+
|+  style="text-align: left;" | Literature values
 
! Value
 
! Value
 
! Units
 
! Units
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
Line 113: Line 138:
 
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
 
|<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>
 
human proteome'' Nature, 2014 509, 582–587]</ref>
Line 123: Line 149:
 
pH: Unknown
 
pH: Unknown
 
Temperature: Unknown
 
Temperature: Unknown
 +
|2048
 
|Unknown
 
|Unknown
 
|-
 
|-
Line 128: Line 155:
 
|ppm
 
|ppm
 
|Human
 
|Human
−
|Expression Vector: Skin
+
|Expression Vector: Oral Cavity
 
Enzyme: PTGR2
 
Enzyme: PTGR2
 
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
 
|<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>
 
human proteome'' Nature, 2014 509, 582–587]</ref>
Line 137: Line 165:
 
|}
 
|}
  
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PTGR-2 concentration distribution
 +
! Mode (ppm) !! Mode (mM) !! Confidence Interval  !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 8.65E+01 || 4.79E-04|| 1.45E+00 || 4.58E+00 || 3.47E-01
 +
|}
 +
 +
[[Image:168.jpg|none|thumb|500px|The estimated probability distribution for PTGR-2 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"  
 
{|class="wikitable"  
−
|+  style="text-align: left;" | Gibbs Free energy
+
|+  style="text-align: left;" | Literature values 
−
! Value
+
! Gibbs Free energy
 
! Units
 
! Units
 
! Species
 
! Species
 
! Notes
 
! Notes
 +
! Weight
 
! Reference
 
! Reference
 
|-
 
|-
−
| X
+
| 3.6006165
−
| Y
+
| kcal/mol
−
| Z
+
|Unspecified
−
| A
+
|Calculations with a Gaussian98 suite of programs
−
| B
+
Enzyme: COX (Unspecific)
 +
Substrate: Arachidonate
 +
Temperature: 298.15 K
 +
Pressure: 1 bar
 +
|64
 +
|<ref name="Silva2003”>[http://link.springer.com/article/10.1007/s00214-003-0476-9 P. Silva, "A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase" Theor Chem Acc (2003) 110: 345]</ref>
 +
|}
 +
 
 +
{| class="wikitable"
 +
|+  style="text-align: left;" | Description of the PTGR-2 Keq distribution
 +
! Mode !! Confidence Interval  !! Location parameter (µ) !! Scale parameter (σ)
 +
|-
 +
| 2.28E-03 || 1.00E+01 || -5.29E+00 || 8.91E-01
 
|}
 
|}
  
 +
[[Image:80.jpg|none|thumb|500px|The estimated probability distribution for PTGR-2 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.  ]]
 +
 +
===Misch===
  
 
{|class="wikitable"  
 
{|class="wikitable"  
Line 188: Line 242:
 
Temperature:  37 ◦C
 
Temperature:  37 ◦C
 
Substrate: 15-Keto-PGE2
 
Substrate: 15-Keto-PGE2
−
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2, Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>  
+
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 "Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2", Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>  
 
|-
 
|-
 
| 66.73 ± 1.36
 
| 66.73 ± 1.36
Line 200: Line 254:
 
Temperature:  37 ◦C
 
Temperature:  37 ◦C
 
Substrate: NADPH
 
Substrate: NADPH
−
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2, Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>  
+
| <ref name="Wu2008"> [https://www.ncbi.nlm.nih.gov/pubmed/19000823 "Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2", Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.]</ref>  
 
|-
 
|-
 
|}
 
|}

Latest revision as of 11:09, 2 November 2019

Return to overview

The second step of the catabolic pathway of prostanoids is the reduction of the conjugated α, β-unsaturated double bond at C13, by 13, 15-ketoprostglandin reductase, also known as prostaglandin reductase. There are two isoforms of this protein, prostaglandin reductase 1 (PTGR-1) and prostaglandin reductase 2 (PTGR-2). Prostaglandin reductase 1 (PTGR-1) can accept a wide variety of prostaglandins as substrates. Prostaglandin reductase 2 (PTGR-2) has the highest affinity for 15-keto-PGE2, but also accepts a wide variety of prostaglandins as a substrate [1].

Reaction

Chemical equation

15-Keto-PGE2 + NAD(P)+ \rightleftharpoons 13,14-Dihydro-15-Keto-PGE2 + NAD(P)H

Rate equation

R69.PNG

Parameters

Kms

Literature values
Value Units Species Notes Weight Reference
0.01121 ± 0.00014 mM Human Method: In vitro

Organism: Human Expression vector: E.coli Enzyme: PTGR2 pH: 7.5 Temperature: 37 ◦C Substrate: 15-Keto-PGE2

"For determining the KM and Vmax values for NADPH, 15-keto-PGE2 at a final concentration of 200 mM was used with different concentrations of NADPH (0–60 mM)."

512 [2]
0.01587 ± 0.00171 mM Human Method: In vitro

Organism: Human Expression vector: E.coli Enzyme: e PTGR2 pH: 7.5 Temperature: 37 ◦C Substrate: NADPH

"For determining the KM and Vmax values for NADPH, 15-keto-PGE2 at a final concentration of 200 mM was used with different concentrations of NADPH (0–60 mM)."

512 [2]


Description of the PTGR-2 Kms distribution
Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
1.20E-02 4.92E+00 -3.97E+00 6.71E-01
The estimated probability distribution for PTGR-2 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 PTGR-2 Kmp distribution
Mode (mM) Location parameter (µ) Scale parameter (σ)
1.19E-02 -3.97E+00 6.81E-01
The estimated probability distribution for PTGR-2 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

Note: Turnover values from EC 1.3.1.48 - 13,14-dehydro-15-oxoprostaglandin 13-reductase

Literature values
Value Units Species Notes Weight Reference
11.4 ± 0.9 min-1 Mouse Method: In vitro

Organism: Mouse Expression vector: Enzyme: 13,14-dehydro-15-oxoprostaglandin 13-reductase pH: 7.4 Temperature: 37 ◦C Substrate: 15-Ketoprostaglandin E2

384 [2]
Description of the PTGR-2 kcat distribution
Mode (min-1) Confidence Interval Location parameter (µ) Scale parameter (σ)
1.14E+01 9.86E+00 3.22E+00 8.87E-01
The estimated probability distribution for PTGR-2 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
162 ppm Human Expression Vector: Skin

Enzyme: PTGR2 pH: 7.5 Temperature: 37 °C

2048 [3]
80.9 ppm Human Expression Vector: Skin

Enzyme: PTGR2 pH: Unknown Temperature: Unknown

2048 Unknown
74.1 ppm Human Expression Vector: Oral Cavity

Enzyme: PTGR2 pH: 7.5 Temperature: 37 °C

1024 [3]
Description of the PTGR-2 concentration distribution
Mode (ppm) Mode (mM) Confidence Interval Location parameter (µ) Scale parameter (σ)
8.65E+01 4.79E-04 1.45E+00 4.58E+00 3.47E-01
The estimated probability distribution for PTGR-2 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 Units Species Notes Weight Reference
3.6006165 kcal/mol Unspecified Calculations with a Gaussian98 suite of programs

Enzyme: COX (Unspecific) Substrate: Arachidonate Temperature: 298.15 K Pressure: 1 bar

64 [4]
Description of the PTGR-2 Keq distribution
Mode Confidence Interval Location parameter (µ) Scale parameter (σ)
2.28E-03 1.00E+01 -5.29E+00 8.91E-01
The estimated probability distribution for PTGR-2 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.

Misch

Half Life
Value Units Species Notes Reference
9.9 +/-0.2 minutes Dog In vivo

Temperature:37 pH:7

[5]
Vmax
Value Units Species Notes Reference
159.23 ± 0.71 nmol min-1 mg-1 Human Method: In vitro

Organism: Human Expression vector: E.coli Enzyme: PTGR2 pH: 7.5 Temperature: 37 ◦C Substrate: 15-Keto-PGE2

[2]
66.73 ± 1.36 nmol min-1 mg-1 Human Method: In vitro

Organism: Human Expression vector: E.coli Enzyme: PTGR2 pH: 7.5 Temperature: 37 ◦C Substrate: NADPH

[2]

References

  1. ↑ Wu, Yu-Hauh Ko, Tzu-Ping Guo, Rey-Ting Hu, Su-Ming Chuang, Lee-Ming Wang, Andrew H J., Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2,Structure (2008), 16, 1714-1723.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 "Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2", Structure. 2008 Nov 12;16(11):1714-23. doi: 10.1016/j.str.2008.09.007.
  3. ↑ 3.0 3.1 [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]
  4. ↑ P. Silva, "A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase" Theor Chem Acc (2003) 110: 345
  5. ↑ W. Bothwell, "A radioimmunoassay for the unstable pulmonary metabolites of prostaglandin E1 and E2: an indirect index of their in vivo disposition and pharmacokinetics" Journal of Pharmacology and Experimental Therapeutics February 1982, 220 (2) 229-235
Retrieved from ‘http://www.systemsbiology.ls.manchester.ac.uk/wiki/index.php?title=Transformation_of_15-Keto-PGE2_to_13,14-Dihydro-15-Keto-PGE2&oldid=7522’