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Cluster information : Rifamycin


close this sectionCompound

Entry nameRifamycin
PKS TypeTypeI modular
Starter Unit3-amino-5-hydroxybenzoic acid (AHBA)
Chain Length11
Sugar Unitnone
ClassificationAnsamycin
ActivityAntibacterial
CompositionSV: C37H47NO12
Rifamycin

close this sectionOriginal source

Organism
StrainS699
Contig
Click on the icon to see Genetic map.

close this sectionPKS/NRPS Module

Rifam_00210
rifA
0
1 methylmalonyl-CoA
2 malonyl-CoA
3 methylmalonyl-CoA
Rifam_00220
rifB
4 methylmalonyl-CoA
5 methylmalonyl-CoA
6 methylmalonyl-CoA
Rifam_00230
rifC
7 methylmalonyl-CoA
Rifam_00240
rifD
8 methylmalonyl-CoA
Rifam_00250
rifE
9 malonyl-CoA
10 methylmalonyl-CoA
A34..436
PCP541..611
KS632..1004
AT1144..1453
dh1489..1634
KR1829..2005
ACP2104..2174
KS2195..2568
AT2717..3025
ACP3077..3151
KS3171..3546
AT3694..4008
kr4307..4475
ACP4580..4650
KS35..411
AT561..877
DH923..1085
KR1346..1519
ACP1624..1694
KS1717..2090
AT2241..2548
dh2592..2726
KR2954..3126
ACP3231..3301
KS3322..3698
AT3847..4160
dh4207..4369
KR4657..4833
ACP4932..5002
KS36..408
AT555..868
dh911..1070
KR1334..1509
ACP1617..1687
KS34..410
AT563..879
dh911..1107
KR1300..1475
ACP1575..1645
KS31..402
AT554..872
DH918..1081
KR1338..1513
ACP1610..1680
KS1702..2076
AT2228..2541
DH2585..2748
KR3054..3230
ACP3336..3406

close this sectionReference

3-Amino-5-hydroxybenzoic acid synthase, the terminal enzyme in the formation of the precursor of mC7N units in rifamycin and related antibiotics.
Kim CG, Yu TW, Fryhle CB, Handa S, Floss HG
[PMID: 9497318]J Biol Chem. 273 (1998) 6030-40
Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699.
August PR, Tang L, Yoon YJ, Ning S, Muller R, Yu TW, Taylor M, Hoffmann D, Kim CG, Zhang X, Hutchinson CR, Floss HG
[PMID: 9512878]Chem Biol. 5 (1998) 69-79
Direct evidence that the rifamycin polyketide synthase assembles polyketide chains processively.
Yu TW, Shen Y, Doi-Katayama Y, Tang L, Park C, Moore BS, Richard Hutchinson C, Floss HG
[PMID: 10430893]Proc Natl Acad Sci U S A. 96 (1999) 9051-6
Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase.
Eads JC, Beeby M, Scapin G, Yu TW, Floss HG
[PMID: 10433690]Biochemistry. 38 (1999) 9840-9
Thioesterases and the premature termination of polyketide chain elongation in rifamycin B biosynthesis by Amycolatopsis mediterranei S699.
Doi-Katayama Y, Yoon YJ, Choi CY, Yu TW, Floss HG, Hutchinson CR
[PMID: 10908112]J Antibiot (Tokyo). 53 (2000) 484-95
Mutational analysis and reconstituted expression of the biosynthetic genes involved in the formation of 3-amino-5-hydroxybenzoic acid, the starter unit of rifamycin biosynthesis in amycolatopsis Mediterranei S699.
Yu TW, Muller R, Muller M, Zhang X, Draeger G, Kim CG, Leistner E, Floss HG
[PMID: 11278540]J Biol Chem. 276 (2001) 12546-55
The loading module of rifamycin synthetase is an adenylation-thiolation didomain with substrate tolerance for substituted benzoates.
Admiraal SJ, Walsh CT, Khosla C
[PMID: 11352749]Biochemistry. 40 (2001) 6116-23
Biosynthesis of 1-deoxy-1-imino-D-erythrose 4-phosphate: a defining metabolite in the aminoshikimate pathway.
Guo J, Frost JW
[PMID: 11804477]J Am Chem Soc. 124 (2002) 528-9
Expression and purification of the rifamycin amide synthase, RifF, an enzyme homologous to the prokaryotic arylamine N-acetyltransferases.
Pompeo F, Mushtaq A, Sim E
[PMID: 11812235]Protein Expr Purif. 24 (2002) 138-51
The loading and initial elongation modules of rifamycin synthetase collaborate to produce mixed aryl ketide products.
Admiraal SJ, Khosla C, Walsh CT
[PMID: 11955082]Biochemistry. 41 (2002) 5313-24
Kanosamine biosynthesis: a likely source of the aminoshikimate pathway's nitrogen atom.
Guo J, Frost JW
[PMID: 12207504]J Am Chem Soc. 124 (2002) 10642-3
Characterization of the early stage aminoshikimate pathway in the formation of 3-amino-5-hydroxybenzoic acid: the RifN protein specifically converts kanosamine into kanosamine 6-phosphate.
Arakawa K, Muller R, Mahmud T, Yu TW, Floss HG
[PMID: 12207505]J Am Chem Soc. 124 (2002) 10644-5
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.
Xu J, Mahmud T, Floss HG
[PMID: 12623077]Arch Biochem Biophys. 411 (2003) 277-88
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.
Xiong Y, Wu X, Mahmud T
[PMID: 15791687]Chembiochem. 6 (2005) 834-7
Identification of tailoring genes involved in the modification of the polyketide backbone of rifamycin B by Amycolatopsis mediterranei S699.
Xu J, Wan E, Kim CJ, Floss HG, Mahmud T
[PMID: 16079331]Microbiology. 151 (2005) 2515-28
RifP; a membrane protein involved in rifamycin export in Amycolatopsis mediterranei.
Absalon AE, Fernandez FJ, Olivares PX, Barrios-Gonzalez J, Campos C, Mejia A
[PMID: 17351715]Biotechnol Lett. 29 (2007) 951-8
Structure and functional analysis of RifR, the type II thioesterase from the rifamycin biosynthetic pathway.
Claxton HB, Akey DL, Silver MK, Admiraal SJ, Smith JL
[PMID: 19103602]J Biol Chem. 284 (2009) 5021-9
The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review.
Floss HG, Yu TW, Arakawa K
[PMID: 21081954]J Antibiot (Tokyo). 64 (2011) 35-44
Stereochemistry of reductions catalyzed by methyl-epimerizing ketoreductase domains of polyketide synthases.
You YO, Khosla C, Cane DE
[PMID: 23659177]J Am Chem Soc. 135 (2013) 7406-9
Coupled methyl group epimerization and reduction by polyketide synthase ketoreductase domains. Ketoreductase-catalyzed equilibrium isotope exchange.
Garg A, Khosla C, Cane DE
[PMID: 24161343]J Am Chem Soc. 135 (2013) 16324-7
Structure and Stereospecificity of the Dehydratase Domain from the Terminal Module of the Rifamycin Polyketide Synthase.
Gay D, You YO, Keatinge-Clay A, Cane DE
[PMID: 24274103]Biochemistry. (2013)
Modification of Rifamycin Polyketide Backbone Leads to Improved Drug Activity Against Rifampicin-Resistant Mycobacterium tuberculosis*
Nigam A, Almabruk KH, Saxena A, Yang J, Mukherjee U, Kaur H, Kohli P, Kumari R, Singh P, Zakharov LN, Singh Y, Mahmud T, Lal R
[PMID: 24923585]J Biol Chem. (2014)
Substrate structure-activity relationships guide rational engineering of modular polyketide synthase ketoreductases.
Bailey CB, Pasman ME, Keatinge-Clay AT
[PMID: 26568113]Chem Commun (Camb). 52 (2016) 792-5
Protein-Protein Interactions, Not Substrate Recognition, Dominate the Turnover of Chimeric Assembly Line Polyketide Synthases.
Klaus M, Ostrowski MP, Austerjost J, Robbins T, Lowry B, Cane DE, Khosla C
[PMID: 27246853]J Biol Chem. 291 (2016) 16404-15

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Compound nameGenomic
nucleotide
sequence
Nucleotide
sequences of the
coding regions
Translation of the
coding sequences
List of genes/ORFsGBK
Rifamycin
Genomic nucleotide sequence
111 KB
Nucleotide sequences of the coding regions
110 KB
Translation of the coding sequences
39 KB
List of genes/ORFs
8 KB

 

 
GenBank format
217 KB

close this sectionHistory

  • 2016-12-27[Update]
  • 2014-06-25[Update]
  • 2013-12-27[Update]
  • 2013-09-04[Update]
  • 2013-05-28[Update]
  • 2012-10-02[Update]
  • 2012-03-28[Release]