Category:PK

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==Classification==
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{| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
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===3-4th digits===
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|+ Table 1. Polyketide Classification
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−
|-
+
−
!colspan="3"|1st Class
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−
|- valign="top"
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−
|align="center"|[[:Category:PK4|PK4: Four C<sub>2</sub> Units]]<br/>
+
−
orsellinic acid, 6-methylsalicylic acid, triacetic acid lactone, asperlin, usnic acid, methylphloracetophenone, penicillic acid, patulin
+
−
 
+
−
|align="center"|[[:Category:PK5|PK5: Five C<sub>2</sub> Units]]<br/>
+
−
citrinin, aflatoxin, augenone, sepedonin, stipitatonic acid
+
−
 
+
−
|align="center"|[[:Category:PK6|PK6: Six C<sub>2</sub> Units]]<br/>
+
−
plumbagin, 7-methyljuglone, juglone, variotin
+
−
 
+
−
|- valign="top"
+
−
|align="center"|[[:Category:PK7|PK7: Seven and eight C<sub>2</sub> Units]]<br/>
+
−
''Anthraquinone rings''<br/>
+
−
griseofulvin, rubrofusarin, emodin, alizarin, pachybasin, xanthone, versicolorin A, aflatoxin B1, sterigmatocystin, tajixanthone
+
−
 
+
−
|align="center"|[[:Category:PK9|PK9: Nine C<sub>2</sub> Units]]<br/>
+
−
''Tetracyclines''<br/>
+
−
terramycin, aureomycin, daunomycin
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−
 
+
−
|-
+
−
|
+
−
|}
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−
</center>
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−
 
+
 
<!----Antimycin
 
<!----Antimycin
 
Elfamycin
 
Elfamycin
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Sorbicillin polymers
 
Sorbicillin polymers
 
---->
 
---->
−
 
  
 
{| class="wikitable"
 
{| class="wikitable"
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|}
 
|}
 
| Acetogenins (LA)
 
| Acetogenins (LA)
−
|
 
 
|-  
 
|-  
 
!colspan="3" style="background:lightgray"| Aromatic and Diels-Alder Related (most often by iterative type II)
 
!colspan="3" style="background:lightgray"| Aromatic and Diels-Alder Related (most often by iterative type II)
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| lovastatin
 
| lovastatin
 
|-
 
|-
−
| aflatoxins<ref></ref>
+
| aflatoxins<ref>foo</ref>
 
|}
 
|}
 
|  
 
|  
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|style="width:200px"|
 
|style="width:200px"|
 
{| class="collapsible collapsed" style="width:200px"
 
{| class="collapsible collapsed" style="width:200px"
−
! 12-membered (M2)
+
! Size12-ring (M2)
 
|-
 
|-
 
|
 
|
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|style="width:200px"|
 
|style="width:200px"|
 
{| class="collapsible collapsed" style="width:200px"
 
{| class="collapsible collapsed" style="width:200px"
−
! 14-membered (M4)
+
! Size14-ring (M4)
 
|-
 
|-
 
| Colletodiol
 
| Colletodiol
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|style="width:200px"|
 
|style="width:200px"|
 
{| class="collapsible collapsed" style="width:200px"
 
{| class="collapsible collapsed" style="width:200px"
−
! 16-membered (M6)
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! Size16-ring (M6)
 
|-
 
|-
 
| Avermectin
 
| Avermectin
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|}
 
|}
 
|}
 
|}
 +
 +
;References
 +
<references/>
 +
===5th digit===
 +
<center>
 +
{| class="wikitable"
 +
|-
 +
!colspan="3" style="background:lightgray"| The number of C<sub>2</sub> unit
 +
|- valign="top"
 +
|align="center" width="200px"|4 Units<br/>
 +
orsellinic acid, 6-methylsalicylic acid, triacetic acid lactone, asperlin, usnic acid, methylphloracetophenone, penicillic acid, patulin
 +
 +
|align="center" width="200px"|5 Units<br/>
 +
citrinin, aflatoxin, augenone, sepedonin, stipitatonic acid
 +
 +
|align="center" width="200px"|6 Units<br/>
 +
plumbagin, 7-methyljuglone, juglone, variotin
 +
 +
|- valign="top"
 +
|align="center" width="200px"|7 & 8 Units<br/>
 +
''Anthraquinone rings''<br/>
 +
griseofulvin, rubrofusarin, emodin, alizarin, pachybasin, xanthone, versicolorin A, aflatoxin B1, sterigmatocystin, tajixanthone
 +
 +
|align="center" width="200px"|9 Units<br/>
 +
''Tetracyclines''<br/>
 +
terramycin, aureomycin, daunomycin
 +
 +
|align="center" width="200px"|>9 Units<br/>
 +
|}
 +
</center>
  
 
==Polyketide Synthase (PKS) ==
 
==Polyketide Synthase (PKS) ==
 +
===Distribution===
 +
PKS members are found in bacteria, fungi, plants, slime mold<ref>Zucko J, Skunca N, Curk T, Zupan B, Long PF et al (2007) "Polyketide synthase genes and the natural products potential of Dictyostelium discoideum" ''Bioinformatics'' 23:2543-49</ref>, Alveolata<ref>Zhu G, LaGier MJ, Stejskal F, Millership JJ, Cai X et al (2002) "Cryptosporidium parvum: the first protist known to encode a putative polyketide synthase" ''Gene'' 298:79-89</ref>, and animals <ref>Castoe TA, Stephens T, Noonan BP, Calestani C (2007) "A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs" ''Gene'' 392:47-58</ref><ref>Calestani C, Rast JP, Davidson EH (2003) "Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening" ''Development'' 130:4587-96</ref>.
 +
 +
;References
 +
<references/>
 +
 +
===Type I, II, and III===
 +
There are three types of PKSs known to date.
 +
 +
'''Type I''' : multiple domains per protein (e.g. Erythromycin biosynthesis <ref> (2001) ''Nat Prod Rep'' 18:380</ref>)
 +
* Bacterial type I is modular.
 +
* Fungal type I is "iterative", i.e., it reuses same active sites through multiple catalytic steps. Non-reducing (NR) type produces aromatic polyketides, and partially reducing type produces others.
 +
'''Type II''' : single domain per protein
 +
* Three proteins (KS&alpha;, KS&beta;, ACP) are repeatedly used for carbon chain elongation, and the chain length is determined by another protein, CLF.
 +
* In bacteria, products are aromatic (e.g. chiorotetracycline, pradimicin).
 +
'''Type III''' : chalcone synthase-like in plants
 +
* Discovered in plants, but later found in bacteria<ref>Moore BS, Hopke JN (2001) Discovery of a new bacterial polyketide biosynthetic pathway ''Chembiochem'' 2:35-8</ref>
  
 
{| class="wikitable"
 
{| class="wikitable"
−
!species || Actinomycetes || Cyanobacteria || &gamma;-Proteobacteria || Fungi || Dinoflagellates
+
!Species || Actinomycetes || Cyanobacteria || &gamma;-Proteobacteria || Fungi || Dinoflagellates
−
|-
+
|- align="center"
 
!Type-I PKS
 
!Type-I PKS
−
| &Omicron; || &Omicron; || &Omicron; || &Chi; || &Omicron;
+
| &Omicron; || &Omicron; || &Omicron; || &Omicron; || &Omicron;
−
|-
+
|- align="center"
 
!Type-II PKS
 
!Type-II PKS
−
| &Omicron; || &Chi; || &Chi; || &Omicron; || &Chi;
+
| &Omicron; || &Chi; || &Chi; || &Chi; || &Chi;
−
|-
+
|- align="center"
 
!NRPS
 
!NRPS
 
| &Omicron; || &Omicron; || &Omicron; || &Omicron; || &Chi;
 
| &Omicron; || &Omicron; || &Omicron; || &Omicron; || &Chi;
−
|-
+
|- align="center"
 
!deoxysugar
 
!deoxysugar
 
| &Omicron; || &Chi; || &Chi; || &Chi; || &Chi;
 
| &Omicron; || &Chi; || &Chi; || &Chi; || &Chi;
−
|-
+
|- align="center"
 
!Terpene
 
!Terpene
 
| &Delta; || &Chi; || &Chi; || &Omicron; || &Chi;
 
| &Delta; || &Chi; || &Chi; || &Omicron; || &Chi;
 
|}
 
|}
−
 
−
===Type I PKS (non-iterative)===
 
−
 
−
* Multi catalytic domains exist in a single protein
 
−
* Chain length is determined by the number of catalytic domains.
 
−
* Products are non-aromatic and have larger masses.
 
−
 
−
Ref. Erythromycin biosynthesis in ''Nat Prod Rep'' '''18''', 380 (2001)
 
−
 
−
===Type II PKS (iterative)===
 
−
 
−
* Three proteins (KS&alpha;, KS&beta;, ACP) are repeatedly used for carbon chain elongation.
 
−
* Chain length is determined by another protein, CLF.
 
−
* In bacteria, products are aromatic (e.g. chiorotetracycline, pradimicin).
 
−
* In fungi, products are both non-aromatic and aromatic.
 
  
 
===Non-ribosomal peptide synthase (NRPS)===
 
===Non-ribosomal peptide synthase (NRPS)===
−
 
 
Coupling with PKS and NRPS
 
Coupling with PKS and NRPS
  
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* rapamycin
 
* rapamycin
  
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==PKS in Fungi==
+
===Decoration===
−
* both aromatic and non-aromatic compounds are generated by iterative PKS
+
−
* methyl branch is transferred from methionine, not methylmalonyl CoA
+
−
 
+
−
Ref. Dewick, PM ''Medicinal Natural Products'' (2009)
+
−
 
+
−
 
+
−
==Decoration==
+
 
deoxysugars
 
deoxysugars
  
 
deoxygenation, c-methylation, amination, n-methylation, ketosugar,
 
deoxygenation, c-methylation, amination, n-methylation, ketosugar,
  
−
==Unusual structures==
+
===Unusual structures===
 
{| class="wikitable"
 
{| class="wikitable"
 
! Phoma
 
! Phoma

Revision as of 11:28, 19 December 2010

Polyketide Top Species List UniRef90 Class UniRef50 Class Gene Class Domains
(by CDD) 		Domains
(by MAPSI)

Polyketide (ポリケチド)

Contents

Class Overview

Polyketides are synthesized through the polymerization of acetyl units (β-ketomethylene) as in fatty acid biosynthesis. Typical starter units are short-chain fatty acids (e.g. acetyl-CoA or propionyl-CoA), on to which extender units (e.g. malonyl-CoA or methylmalonyl-CoA) are repeatedly polymerized. The key reactions for the chain extension are:

  • Claisen condensation by β-ketoacyl synthase (KS)
  • an acyltransferase (AT), and
  • an acyl carrier protein (ACP).

After elongation, β-ketone is reduced. In fatty acid biosynthesis, the chain is fully reduced by the following three steps:

  • Reduction to an alcohol by ketoreductase (KR),
  • Dehydration to the conjugated ester by dehydratase (DH), and
  • Reduction of the double bond by enoyl reductase (ER).
In polyketide synthase, the reduction is patial.

Finally, the chain is terminated by a thioesterase (TE) activity and allows Claisen cyclization (CYC).

Classification

3-4th digits

Linear Chain and Related (L)
Acetogenins (LA)
Aromatic and Diels-Alder Related (most often by iterative type II)
Macrolides (most often by non-iterative type I)
References
  1. ↑ foo
  2. ↑ 6-deoxy sugars (L-cladinose and D-desosamine) are attached.
  3. ↑ http://www.indiana.edu/~drwchem/pdfs/50.pdf
  4. ↑ =Pimaricin

5th digit

The number of C2 unit
4 Units

orsellinic acid, 6-methylsalicylic acid, triacetic acid lactone, asperlin, usnic acid, methylphloracetophenone, penicillic acid, patulin

5 Units

citrinin, aflatoxin, augenone, sepedonin, stipitatonic acid

6 Units

plumbagin, 7-methyljuglone, juglone, variotin

7 & 8 Units

Anthraquinone rings
griseofulvin, rubrofusarin, emodin, alizarin, pachybasin, xanthone, versicolorin A, aflatoxin B1, sterigmatocystin, tajixanthone

9 Units

Tetracyclines
terramycin, aureomycin, daunomycin

>9 Units

Polyketide Synthase (PKS)

Distribution

PKS members are found in bacteria, fungi, plants, slime mold[1], Alveolata[2], and animals [3][4].

References
  1. ↑ Zucko J, Skunca N, Curk T, Zupan B, Long PF et al (2007) "Polyketide synthase genes and the natural products potential of Dictyostelium discoideum" Bioinformatics 23:2543-49
  2. ↑ Zhu G, LaGier MJ, Stejskal F, Millership JJ, Cai X et al (2002) "Cryptosporidium parvum: the first protist known to encode a putative polyketide synthase" Gene 298:79-89
  3. ↑ Castoe TA, Stephens T, Noonan BP, Calestani C (2007) "A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs" Gene 392:47-58
  4. ↑ Calestani C, Rast JP, Davidson EH (2003) "Isolation of pigment cell specific genes in the sea urchin embryo by differential macroarray screening" Development 130:4587-96

Type I, II, and III

There are three types of PKSs known to date.

Type I : multiple domains per protein (e.g. Erythromycin biosynthesis [1])

  • Bacterial type I is modular.
  • Fungal type I is "iterative", i.e., it reuses same active sites through multiple catalytic steps. Non-reducing (NR) type produces aromatic polyketides, and partially reducing type produces others.

Type II : single domain per protein

  • Three proteins (KSα, KSβ, ACP) are repeatedly used for carbon chain elongation, and the chain length is determined by another protein, CLF.
  • In bacteria, products are aromatic (e.g. chiorotetracycline, pradimicin).

Type III : chalcone synthase-like in plants

  • Discovered in plants, but later found in bacteria[2]
Species Actinomycetes Cyanobacteria γ-Proteobacteria Fungi Dinoflagellates
Type-I PKS Ο Ο Ο Ο Ο
Type-II PKS Ο Χ Χ Χ Χ
NRPS Ο Ο Ο Ο Χ
deoxysugar Ο Χ Χ Χ Χ
Terpene Δ Χ Χ Ο Χ

Non-ribosomal peptide synthase (NRPS)

Coupling with PKS and NRPS

  • vancomycin ()
  • leinamycin (Curr opin chem biol 7:285, 2003)
  • pseurotin (chem bio chem 8:1736-1743, 2007)
  • curacin (curr opin chem biol 13:216, 2009)
  • epothilone
  • rapamycin

Decoration

deoxysugars

deoxygenation, c-methylation, amination, n-methylation, ketosugar,

Unusual structures

Phoma zaragozic acid, phomoidoride Streptomyces yatakemycin, leinamycin, saframycin, neocarzinostatin, staurosporin, FR182877 Other bacteria PKS-NRPS hybrid type

Curacin A (Lyngbya), Shiphonazole (Herpetosiphon), Jamaicamide A (Lyngbya), Cylindrospermopsin (Cylindrospermopsis)



Cite error: <ref> tags exist, but no <references/> tag was found

Subcategories

This category has only the following subcategory.

P

  • [×] PKS‎ (empty)
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