MetaCyc Protein: rifamycin polyketide synthase E subunit dimer

Gene: rifE Accession Number: G-10776 (MetaCyc)

Species: Amycolatopsis mediterranei

Component of: rifamycin polyketide synthase (extended summary available)

Subunit composition of rifamycin polyketide synthase E subunit dimer = [RifE]2
         rifamycin polyketide synthase E subunit = RifE

The rifE gene product encodes modules 9 and 10 which contain ketosynthase, acyltransferase, dehydratase, ketoreductase and acyl carrier protein domains. These modules extend the polyketide chain from a nonaketide to a decaketide, and an undecaketide, respectively. Module 9 uses malonyl-CoA rather than (S)-methylmalonyl-CoA as a chain extender unit (reviewed in [Floss05]).

Gene Citations: [August98, Schupp98, Xu05]

Molecular Weight of Polypeptide: 353.73 kD (from nucleotide sequence)

Unification Links: Protein Model Portal:O54593, SMR:O54593, String:749927.AMED_0621, UniProt:O54593

Relationship Links: Entrez-Nucleotide:RELATED-TO:AF040570, InterPro:IN-FAMILY:IPR001227, InterPro:IN-FAMILY:IPR002198, InterPro:IN-FAMILY:IPR006162, InterPro:IN-FAMILY:IPR009081, InterPro:IN-FAMILY:IPR013968, InterPro:IN-FAMILY:IPR014030, InterPro:IN-FAMILY:IPR014031, InterPro:IN-FAMILY:IPR014043, InterPro:IN-FAMILY:IPR015083, InterPro:IN-FAMILY:IPR016035, InterPro:IN-FAMILY:IPR016036, InterPro:IN-FAMILY:IPR016039, InterPro:IN-FAMILY:IPR016040, InterPro:IN-FAMILY:IPR018201, InterPro:IN-FAMILY:IPR020801, InterPro:IN-FAMILY:IPR020806, InterPro:IN-FAMILY:IPR020807, InterPro:IN-FAMILY:IPR020841, Panther:IN-FAMILY:PTHR11712, PDB:Structure:4LN9, Pfam:IN-FAMILY:PF00106, Pfam:IN-FAMILY:PF00109, Pfam:IN-FAMILY:PF00550, Pfam:IN-FAMILY:PF00698, Pfam:IN-FAMILY:PF02801, Pfam:IN-FAMILY:PF08990, Pfam:IN-FAMILY:PF14765, Prosite:IN-FAMILY:PS00012, Prosite:IN-FAMILY:PS00606, Prosite:IN-FAMILY:PS50075, Smart:IN-FAMILY:SM00822, Smart:IN-FAMILY:SM00823, Smart:IN-FAMILY:SM00825, Smart:IN-FAMILY:SM00826, Smart:IN-FAMILY:SM00827

Reactions known to consume the compound:

aclacinomycin biosynthesis , daunorubicin biosynthesis :
propanoyl-CoA + 9 malonyl-CoA + polyketide synthase + 9 H+ → 3,5,7,9,11,13,15,17,19-nonaoxohenicosanoyl-[acp] + 9 CO2 + 10 coenzyme A

actinorhodin biosynthesis :
8 malonyl-CoA + polyketide synthase + 8 H+ → a 3,5,7,9,11,13,15-hepta-oxo-hexadecanoyl-[PKS-acp] + 8 CO2 + 8 coenzyme A

mithramycin biosynthesis :
polyketide synthase + acetyl-CoA + 9 malonyl-CoA + 9 H+ → 2-[4,5,7,10-tetrahydroxy-3-(3-oxobutanoyl)anthracen-2-yl]acetyl-[PKS-acp] + 9 CO2 + 10 coenzyme A + 3 H2O

rifamycin B biosynthesis :
3-amino-5-hydroxybenzoate + ATP + polyketide synthase → a 1-(3-amino-5-hydroxyphenyl)ethan-1-one -[PKS-acp] + AMP + diphosphate

zwittermicin A biosynthesis :
a fatty acid + L-asparagine + L-serine + malonyl-CoA + an aminomalonyl-[seryl-carrier protein] + a (2R)-2-hydroxymalonyl-[acp] + β-ureidoalanine + L-alanine + polyketide synthase + 8 NADPH + oxygen + 12 H+ → proto-zwittermicin A-L-alaninyl-[PKS] + 2 CO2 + a holo-[seryl-carrier protein] + a holo-[acyl-carrier protein] + coenzyme A + 8 NADP+ + 9 H2O

Reactions known to produce the compound:

aclacinomycin biosynthesis , daunorubicin biosynthesis :
aklanonate anthrone-[acp] + oxygen → aklanonate + polyketide synthase + H+

actinorhodin biosynthesis :
4-(3'-acetyl-5'-hydroxy-4'-oxo-1',4'-dihydronapthalen-2'-yl)-3-oxobutanoate-[PKS-acp] + H2O → 4-(3'-acetyl-5'-hydroxy-4'-oxo-1',4'-dihydronapthalen-2'-yl)-3-oxobutanoate + polyketide synthase + H+

mithramycin biosynthesis :
(2S)-2-hydroxy-2-[4,5,7,10-tetrahydroxy-3-(3-oxobutanoyl)anthracen-2-yl]acetyl-[PKS-acp] → (4S)-2-acetyl-3,4,8,10,11,12-hexahydroxy-1,4-dihydrotetracen-1-one + polyketide synthase + H+

rifamycin B biosynthesis :
a 3-amino-5,7-dihydroxy-6-methyl-8-[(2E,13E,15E)-5,7,9,11-tetrahydroxy-2,4,6,8,10,12,16-heptamethyl-17-oxooctadeca-2,13,15-trienoyl]-1,4,5,6-tetrahydronaphthalene-1,4-dione-[PKS-acp] → proansamycin X + polyketide synthase + H+

zwittermicin A biosynthesis :
proto-zwittermicin A-L-alaninyl-[PKS] + L-leucine + L-methionine + NADPH + oxygen → proto-zwittermicin A + pyruvoyl-L-leucyl-L-methionine + polyketide synthase + NADP+ + 2 H2O

In Reactions of unknown directionality:

Not in pathways:
2-oxo-2-[4,5,7,10-tetrahydroxy-3-(3-oxobutanoyl)anthracen-2-yl]acetyl-[PKS-acp] + acetoacetate = 1-[4,5,7,10-tetrahydroxy-3-(3-oxobutanoyl)anthracen-2-yl]pentane-1,2,4-trione + polyketide synthase + CO2 + H+

Gene-Reaction Schematic

Gene-Reaction Schematic

Created 30-Jul-2008 by Fulcher CA, SRI International

Subunit of: rifamycin polyketide synthase

Synonyms: rifamycin polyketide synthetase, rifamycin PKS

Species: Amycolatopsis mediterranei

Subunit composition of rifamycin polyketide synthase = [(RifA)2][(RifB)2][(RifC)2][(RifD)2][(RifE)2]
         rifamycin polyketide synthase A subunit dimer = (RifA)2
                 rifamycin polyketide synthase A subunit = RifA
         rifamycin polyketide synthase B subunit dimer = (RifB)2
                 rifamycin polyketide synthase B subunit = RifB
         rifamycin polyketide synthase C subunit dimer = (RifC)2
                 rifamycin polyketide synthase C subunit = RifC
         rifamycin polyketide synthase D subunit dimer = (RifD)2
                 rifamycin polyketide synthase D subunit = RifD
         rifamycin polyketide synthase E subunit dimer = (RifE)2
                 rifamycin polyketide synthase E subunit = RifE

Bacterial polyketide synthases can be broadly classified into three types. Type I are modular polydetide synthases consisting of one or more large, multidomain polypeptides. Polyketide chains are extended in length in a stepwise manner as they are passed from one enzymatically active domain to the next. Type II are iterative polyketide synthases that repetitively use a single set of active sites to assemble a polyketide of controlled chain length. In type III polyketide synthases, the growing chain is not directly attached to the enzyme (in [Ridley08]). See [Fischbach06] for a review of polyketide synthase mechanisms.

This enzyme catalyzes the initial reactions in rifamycin B biosynthesis from 3-amino-5-hydroxybenzoate. It is a type I, modular polyketide synthase encoded by five genes, rifA, rifB, rifC, rifD and rifE. Each gene product encodes a large subunit. Each subunit contains one or more modules, with each module composed of functional domains, although not all domains within a module may be active (reviewed in [Floss05]). The polyketide synthase utilizes 3-amino-5-hydroxybenzoate as a starter unit (see pathway 3-amino-5-hydroxybenzoate biosynthesis) followed by ten rounds of C2 chain extension using two acetate and eight propionate units derived from malonyl-CoA and (S)-methylmalonyl-CoA, to form an undecaketide (in [Xiong05, Xu03, Hartung05]). See pathway rifamycin B biosynthesis.

This enzyme is described as a mixed non-ribosomal peptide synthase/polyketide synthase because its loading module is a non-ribosomal peptide synthase-like adenylation-thiolation didomain and it contains ten polyketide synthase elongation modules. Domains within the modules may include ketosynthase (KS), acyltransferase (AT), dehydratase (DH), ketoreductase (KR) and acyl carrier protein (ACP) domains. The acyl carrier protein domain is also referred to as the thiolation, T, ACP, [acp], or holo-[acyl-carrier protein] domain [Admiraal01, Admiraal02, Admiraal03] and reviewed in [Floss05]. The holo-[acyl carrier protein] domain is created from an apo-[acyl carrier protein] domain that is posttranslationally modified by phosphopantetheinyltransferase-catalyzed covalent attachment of 4'-phosphopantetheine (derived from coenzyme A) to a conserved serine residue (in [Fischbach06]) (see a holo-[acyl-carrier protein] and an apo-[acyl-carrier protein]). Some modules do not contain all of the above domains, for example module 2 contains only the ketosynthase, acyltransferase and acyl carrier protein domains [Tang98].

The quaternary structure of modular polyketide synthases remains under investigation, but it is suggested to be a loosely associated complex of homodimers of the large polypeptide subunits. The subunits associate into homodimers through docking domain contacts at their N- and C-termini [Broadhurst03].

The loading module has been shown to activate 3-amino-5-hydroxybenzoate as an AMP derivative and link it to the acyl carrier protein domain via a thioester linkage to the phosphopantetheinyl moiety of this domain [Admiraal01, Admiraal02, Admiraal03]. The activation by adenylation is a non-ribosomal peptide synthase-like mechanism [Admiraal01]. In module 1 of the polyketide synthase it reacts with a methylmalonyl moiety. Reduction and decarboxylation produce the enzyme-bound ([acp]-) intermediate. The use of (S)-methylmalonyl-CoA or malonyl-CoA as a chain extender unit depends upon the amino acid sequence characteristics of the AT domain within a module. The rifamycin polyketide synthase was determined to use malonyl-CoA in modules 2 and 9 of the rifA and rifE gene products respectively, and (S)-methylmalonyl-CoA in the other modules [Tang98].

This enzyme has also been referred to as rifamycin polyketide synthetase due to its use of ATP in the 3-amino-5-hydroxybenzoate loading reaction catalyzed by the rifA gene product (see below) [Admiraal01].

Created 30-Jul-2008 by Fulcher CA, SRI International

Enzymatic reaction of: 3-amino-5,7-dihydroxy-6-methyl-8-[(2E,13E,15E)-5,7,9,11-tetrahydroxy-2,4,6,8,10,12,16-heptamethyl-17-oxooctadeca-2,13,15-trienoyl]-1,4,5,6-tetrahydronaphthalene-1,4-dione-[PKS-acp] synthase (rifamycin polyketide synthase)

Inferred from experiment

a 3-amino-8-[(2E)-2,4-dimethyl-5-oxohex-2-enoyl]-5,7-dihydroxy-6-methyl-1,4,5,6-tetrahydronaphthalene-1,4-dione -[PKS-acp] + 5 (S)-methylmalonyl-CoA + malonyl-CoA + 6 NADPH + 12 H+ → a 3-amino-5,7-dihydroxy-6-methyl-8-[(2E,13E,15E)-5,7,9,11-tetrahydroxy-2,4,6,8,10,12,16-heptamethyl-17-oxooctadeca-2,13,15-trienoyl]-1,4,5,6-tetrahydronaphthalene-1,4-dione-[PKS-acp] + 6 CO2 + 6 coenzyme A + 6 NADP+ + 2 H2O

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: superpathway of rifamycin B biosynthesis, rifamycin B biosynthesis

This reaction represents a series of six, consecutive polyketide chain extension steps catalyzed by the rifB, rifC, rifD and rifE gene products of the rifamycin polyketide synthase complex (encoded by genes rifA, rifB, rifC, rifD and rifE) (reviewed in [Floss05]).

Following the formation of the cyclized pentaketide substrate shown here, a 3-amino-8-[(2E)-2,4-dimethyl-5-oxohex-2-enoyl]-5,7-dihydroxy-6-methyl-1,4,5,6-tetrahydronaphthalene-1,4-dione -[PKS-acp] (as described in the pathway comments in pathway rifamycin B biosynthesis), six more chain extension steps involving rifamycin polyketide synthase modules 5-10 produce the final acyl carrier protein-bound product, a linear undecaketide with a naphthoquinone ring, a 3-amino-5,7-dihydroxy-6-methyl-8-[(2E,13E,15E)-5,7,9,11-tetrahydroxy-2,4,6,8,10,12,16-heptamethyl-17-oxooctadeca-2,13,15-trienoyl]-1,4,5,6-tetrahydronaphthalene-1,4-dione-[PKS-acp] (click on this object for naming comments).

Cofactors or Prosthetic Groups: 4'-phosphopantetheine [Admiraal02]


Admiraal01: Admiraal SJ, Walsh CT, Khosla C (2001). "The loading module of rifamycin synthetase is an adenylation-thiolation didomain with substrate tolerance for substituted benzoates." Biochemistry 40(20);6116-23. PMID: 11352749

Admiraal02: Admiraal SJ, Khosla C, Walsh CT (2002). "The loading and initial elongation modules of rifamycin synthetase collaborate to produce mixed aryl ketide products." Biochemistry 41(16);5313-24. PMID: 11955082

Admiraal03: Admiraal SJ, Khosla C, Walsh CT (2003). "A Switch for the transfer of substrate between nonribosomal peptide and polyketide modules of the rifamycin synthetase assembly line." J Am Chem Soc 125(45);13664-5. PMID: 14599196

August98: August PR, Tang L, Yoon YJ, Ning S, Muller R, Yu TW, Taylor M, Hoffmann D, Kim CG, Zhang X, Hutchinson CR, Floss HG (1998). "Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699." Chem Biol 5(2);69-79. PMID: 9512878

Broadhurst03: Broadhurst RW, Nietlispach D, Wheatcroft MP, Leadlay PF, Weissman KJ (2003). "The structure of docking domains in modular polyketide synthases." Chem Biol 10(8);723-31. PMID: 12954331

Fischbach06: Fischbach MA, Walsh CT (2006). "Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms." Chem Rev 106(8);3468-96. PMID: 16895337

Floss05: Floss HG, Yu TW (2005). "Rifamycin-mode of action, resistance, and biosynthesis." Chem Rev 105(2);621-32. PMID: 15700959

Hartung05: Hartung IV, Rude MA, Schnarr NA, Hunziker D, Khosla C (2005). "Stereochemical assignment of intermediates in the rifamycin biosynthetic pathway by precursor-directed biosynthesis." J Am Chem Soc 127(32);11202-3. PMID: 16089423

Ridley08: Ridley CP, Lee HY, Khosla C (2008). "Evolution of polyketide synthases in bacteria." Proc Natl Acad Sci U S A 105(12);4595-600. PMID: 18250311

Schupp98: Schupp T, Toupet C, Engel N, Goff S (1998). "Cloning and sequence analysis of the putative rifamycin polyketide synthase gene cluster from Amycolatopsis mediterranei." FEMS Microbiol Lett 159(2);201-7. PMID: 9503613

Tang98: Tang L, Yoon YJ, Choi CY, Hutchinson CR (1998). "Characterization of the enzymatic domains in the modular polyketide synthase involved in rifamycin B biosynthesis by Amycolatopsis mediterranei." Gene 216(2);255-65. PMID: 9729415

Xiong05: Xiong Y, Wu X, Mahmud T (2005). "A homologue of the Mycobacterium tuberculosis PapA5 protein, rif-orf20, is an acetyltransferase involved in the biosynthesis of antitubercular drug rifamycin B by Amycolatopsis mediterranei S699." Chembiochem 6(5);834-7. PMID: 15791687

Xu03: Xu J, Mahmud T, Floss HG (2003). "Isolation and characterization of 27-O-demethylrifamycin SV methyltransferase provides new insights into the post-PKS modification steps during the biosynthesis of the antitubercular drug rifamycin B by Amycolatopsis mediterranei S699." Arch Biochem Biophys 411(2);277-88. PMID: 12623077

Xu05: Xu J, Wan E, Kim CJ, Floss HG, Mahmud T (2005). "Identification of tailoring genes involved in the modification of the polyketide backbone of rifamycin B by Amycolatopsis mediterranei S699." Microbiology 151(Pt 8);2515-28. PMID: 16079331

Yu99: Yu TW, Shen Y, Doi-Katayama Y, Tang L, Park C, Moore BS, Richard Hutchinson C, Floss HG (1999). "Direct evidence that the rifamycin polyketide synthase assembles polyketide chains processively." Proc Natl Acad Sci U S A 96(16);9051-6. PMID: 10430893

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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