Rifam_00230 : CDS information

Location

Organism	Amycolatopsis mediterranei
Strain	S699
Entry name	Rifamycin
Contig	AF040570
Start / Stop / Direction	47,174 / 52,465 / + [in whole cluster] 47,174 / 52,465 / + [in contig]
Location	47174..52465 [in whole cluster] 47174..52465 [in contig]
Type	CDS
Length	5,292 bp (1,763 aa)

Annotation

Category	1.1 PKS
Product	polyketide synthase
Product (GenBank)	RifC
Gene
Gene (GenBank)	rifC
EC number
Keyword
Note
Note (GenBank)	rifamycin polyketide synthase
Reference	ACC O52790 PmId [9512878] Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699. (Chem Biol. , 1998) [10430893] Direct evidence that the rifamycin polyketide synthase assembles polyketide chains processively. (Proc Natl Acad Sci U S A. , 1999) [23659177] Stereochemistry of reductions catalyzed by methyl-epimerizing ketoreductase domains of polyketide synthases. (J Am Chem Soc. , 2013) [24161343] Coupled methyl group epimerization and reduction by polyketide synthase ketoreductase domains. Ketoreductase-catalyzed equilibrium isotope exchange. (J Am Chem Soc. , 2013) [26568113] Substrate structure-activity relationships guide rational engineering of modular polyketide synthase ketoreductases. (Chem Commun (Camb). , 2016) [27246853] Protein-Protein Interactions, Not Substrate Recognition, Dominate the Turnover of Chimeric Assembly Line Polyketide Synthases. (J Biol Chem. , 2016) comment [PMID: 9512878](1998) ansamycin系抗生物質rifamycinの生合成gene clusterの報告。 RifC(1763aa): PKS Module 7 (KS-AT-dh-KR-ACP) AT = methylmalonyl-CoAを利用 Module 7 DH domainは産物の構造上不要。 --- [PMID: 10430893](1999) 同じ著者らのPKSに関する報告。 --- [PMID: 23659177](2013) KR domainによる2-methyl-3-ketoacyl-ACP基質の還元と共に起こる2-methyl基の異性化について調査した報告。 NysKR1, RifKR7, RifKR10はどれも(2S,3S)-2-methyl-3-hydroxypentanoyl-ACPを立体特異的に産生し、2-methyl基の異性化が起こっている。この異性化はACP domainの構造には関係がなく、3-keto基還元の前に起こる。 RifKR7, RifKR10は、NysKR1などその他の(2S,3S)配置をもたらすKR domainsで保存されているTrp and Hisが、Phe and Serで置換されている。 --- [PMID: 24161343](2013) abstract 同位体交換測定を用いて、特異的なPKS KR domainsが持つ内因性のepimerase活性を直接的に確認している。RifKR7も測定されている。 --- [PMID: 26568113](2016) RifKR7での点変異による立体選択性の確認をしている。 --- [PMID: 27246853](2016) キメラPKS作成において、rifamycin PKSのmodule 1, 2, 3, 5, 6, 7を使用している。

PKS/NRPS Module

methylmalonyl-CoA

KS	36..408

AT	555..868

dh	911..1070

KR	1334..1509

ACP	1617..1687

Sequence

>polyketide synthase [RifC]
MVSASYEKVVEALRKSLEEVGTLKKRNRQLADAAGEPIAIVGMACRLPGGVTGPGDLWRL
VAEGGDAVSGFPTDRCWDLDTLFDPDPDHAGTSYTDQGGFLHDAALFDPGFFGISPREAL
AMDPQQRLLLEASWEALEGVGLDPASLQGTDVGVFTGAGGSGYGGGLTGPEMQSFAGTGL
ASSVASGRVSYVFGFEGPAVTIDTACSSSLVAMHLAAQALRQGDCSMALAGGAMVMSGPD
SFVVFSRQRGLATDGRCKAFASGADGMVLAEGISVVVLERLSVARERGHRVLAVLRGSAV
NQDGASNGLTAPNGPSQQRVIRAALANAGIGPSDVDLVEAHGTGTSLGDPIEAQALLATY
GQDRETPLWLGSLKSNIGHTQAAAGVASVIKVVQALRHGVMPPTLHVDEPSSQVDWSEGA
VELLTGSRDWPRGDRPRRAGVSSFGVSGTNVHLIIEEAPEEPAAAVPTSADVVPLVVSAR
STGSLAGQADRLTEVDVPLGHLAGALVAGRAVLEERAVVVAGSAEEARAGLGALARGEAA
PGVVTGTAGKPGKVVWVFPGQGTQWVGMGRELLDASPVFAERIKECAAALDQWTDWSLLD
VLRGDGDLDSVEVLQPACFAVMVGLAAVWESAGVRPDAVVGHSQGEIAAACVSGALTLDD
AAKVVALRSQAIAARLSGRGGMASVALSEDEANARLGLWDGRIEVAAVNGPASVVIAGDA
QALDEALEVLAGDGVRVRQVAVDYASHTRHVEDIRDTLAETLAGITAQAPDVPFRSTVTG
GWVRDADVLDGGYWYRNLRNQVRFGPAVAELLEQGHGVFVEVSAHPVLVQPISELTDAVV
TGTLRRDDGGLRRLLTSMAELFVRGVRVDWATLVPPARVDLPTYAFDHQHFWLRPAAQAD
AVSLGQAAAEHPLLGAVVRLPQSDGLVFTSRLSLRTHPWLADHTIGGVVLFPGTGLVELA
VRAGDEAGCPVLDELVTEAPLVVPGQGGVNVQVTVSGPDQNGLRTVDIHSQRDDVWTRHA
TGTVSATPASSPGFDFTAWPPPDGQRVEIGDFYADLAERGYAYGPLFQGVRAVWQRGEDV
FAEVALPEDRREDAARFGLHPALLDAALQTGTIAAAASGQPGKSVMPFSWNRLALHAVGA
AGLRVRVAPGGPDALTVEAADETGAPVLTMDSLILREVALDQLDTARAGSLYRVDWTPLP
TVDSAVPAGRAEVLEAFGEEPLDLTGRVLAALQAWLSDAAEEARLVVVTRGAVPAGDGVV
SDPAGAAVWGLVRAAQAENPDRFVLLDTDGEVPLEAVLATGEPQLALRGTTFSVPRLARV
TEPAEAPLTFRPDGTVLVSGAGTLGALAARDLVTRHGVRRLVLASRRGRAAEGIDDLVAE
LTGHGAEVTVAACDVSDRDQVAALLKEHALTAVVHTAGVFDAGVTGALTRERLAKVFAPK
VDAANHLDELTRDLDLDAFIVYSSASSIFMGAGSGGYAAANAYLDGLMAARRAAGLPGLS
LAWGPWEQLTGMADTIDDLTLARMSRREGRGGVRALGSADGMELFDAALAAGQALLVPIE
LDLREVRADAAGGGTVPHLLRGLVRAGRQAARTAATEDGGLERRLAGLTVAEQEALLLDL
VRGQVAVVLGHADSSGVRADAAFKDAGFDSLTSVELRNRLRETTGLKLPATLVFDHPNPL
ALARHLRAELAVDEASPADAVLAGLAGLEAAIAAAGAPDGDRITARLRELLKAAEAAEAR
PGTSGDLDTASDEELFALVDGLD

>polyketide synthase [RifC]
GTGGTGAGTGCGTCGTATGAAAAGGTCGTCGAGGCGCTGCGGAAGTCGCTCGAAGAGGTC
GGCACGCTGAAGAAGCGGAACCGGCAGCTCGCCGACGCGGCCGGCGAGCCGATCGCCATC
GTCGGCATGGCCTGCCGGCTGCCCGGTGGCGTCACCGGGCCCGGTGACCTCTGGCGGCTG
GTGGCCGAGGGCGGCGACGCCGTCTCGGGGTTCCCCACCGACCGCTGCTGGGACCTGGAC
ACCCTGTTCGACCCGGATCCCGACCACGCGGGGACGTCGTACACCGACCAGGGCGGCTTC
CTCCACGACGCGGCCCTGTTCGACCCGGGCTTCTTCGGGATTTCGCCGCGCGAGGCGCTG
GCCATGGACCCGCAGCAGCGGTTGCTGCTGGAGGCGTCCTGGGAGGCGCTGGAAGGTGTC
GGCCTCGACCCGGCTTCGTTGCAGGGCACCGACGTCGGCGTGTTCACCGGCGCGGGCGGG
TCGGGCTACGGCGGCGGCCTCACCGGGCCGGAGATGCAGAGTTTCGCGGGCACCGGGCTG
GCCTCGAGCGTGGCTTCGGGCCGGGTGTCCTACGTCTTCGGGTTCGAGGGACCGGCGGTC
ACGATCGACACGGCGTGCTCGTCGTCGCTGGTGGCGATGCACCTCGCCGCGCAGGCCCTG
CGCCAAGGCGACTGCTCGATGGCACTGGCCGGCGGCGCGATGGTGATGTCGGGCCCCGAC
TCCTTCGTCGTCTTCTCCCGGCAGCGGGGGCTGGCCACCGACGGGCGGTGCAAGGCGTTC
GCGTCGGGCGCCGACGGCATGGTGCTCGCCGAGGGCATCAGCGTGGTCGTGCTGGAGCGG
CTTTCGGTCGCGCGGGAACGCGGGCACCGGGTGCTGGCCGTGCTGCGCGGCAGCGCGGTG
AACCAGGATGGCGCGTCGAACGGCCTGACCGCCCCGAACGGCCCTTCCCAGCAGCGCGTG
ATCCGCGCCGCGCTGGCCAACGCCGGAATCGGACCGTCCGATGTGGACCTCGTCGAGGCG
CACGGGACCGGGACGAGCCTGGGTGATCCCATCGAGGCGCAGGCCTTGCTGGCGACCTAC
GGCCAGGACCGGGAGACGCCGTTGTGGCTCGGCTCGCTGAAGTCGAACATCGGGCACACG
CAGGCGGCCGCGGGCGTGGCGAGCGTGATCAAGGTCGTGCAGGCGCTGCGGCACGGCGTC
ATGCCGCCGACCCTGCACGTCGACGAGCCCAGCTCGCAGGTCGACTGGTCCGAAGGCGCG
GTGGAACTGCTGACCGGGAGCCGGGACTGGCCGCGCGGGGACCGGCCGCGCCGGGCCGGG
GTGTCGTCGTTCGGCGTCAGCGGGACGAACGTGCACCTGATCATCGAGGAAGCCCCCGAG
GAGCCCGCTGCGGCCGTGCCGACGTCCGCGGACGTCGTGCCGCTGGTGGTTTCCGCACGC
AGCACGGGTTCCCTGGCCGGTCAGGCCGACCGGCTGACCGAGGTGGACGTCCCCCTCGGA
CACCTCGCCGGGGCGCTGGTGGCCGGGCGCGCGGTGCTCGAGGAACGCGCGGTCGTGGTC
GCCGGTTCGGCCGAAGAAGCCCGCGCGGGGCTGGGTGCGCTGGCTCGCGGTGAAGCCGCG
CCCGGCGTCGTGACCGGGACCGCGGGCAAGCCGGGCAAGGTCGTCTGGGTGTTCCCGGGA
CAGGGGACGCAGTGGGTGGGCATGGGCCGGGAGCTCCTCGACGCGTCCCCGGTGTTCGCC
GAGCGGATCAAGGAGTGCGCGGCGGCACTGGACCAGTGGACCGACTGGTCGCTGCTGGAC
GTCCTGCGTGGTGACGGTGACCTGGATTCTGTCGAGGTGCTGCAGCCCGCGTGCTTCGCG
GTGATGGTGGGGCTGGCCGCGGTCTGGGAGTCGGCGGGGGTCCGGCCGGACGCCGTCGTC
GGCCACTCGCAGGGCGAGATCGCCGCGGCCTGCGTGTCCGGCGCGCTCACCCTCGACGAC
GCCGCGAAGGTGGTGGCCCTGCGCAGCCAGGCGATCGCGGCGCGGCTGTCCGGCCGCGGC
GGGATGGCGTCGGTCGCGTTGAGCGAGGACGAGGCGAACGCACGGCTGGGTTTGTGGGAC
GGCCGGATCGAGGTGGCCGCGGTCAACGGCCCCGCCTCCGTGGTGATCGCGGGGGACGCC
CAAGCCCTCGACGAGGCTTTGGAGGTGCTGGCCGGGGACGGCGTCCGCGTCCGGCAGGTC
GCGGTCGACTACGCCTCCCACACCCGGCACGTCGAGGACATCCGCGACACCCTCGCCGAG
ACGCTGGCCGGGATCACCGCGCAGGCCCCGGACGTGCCGTTCCGCTCCACCGTCACCGGC
GGCTGGGTGCGGGACGCCGACGTCCTGGACGGCGGGTACTGGTACCGCAACCTGCGCAAC
CAGGTCCGGTTCGGCCCGGCCGTGGCCGAGCTGCTCGAGCAGGGCCACGGGGTGTTCGTC
GAGGTCAGCGCCCACCCCGTGCTGGTGCAGCCGATCAGCGAGCTCACCGACGCGGTCGTC
ACCGGGACGCTGCGGCGCGACGACGGCGGCCTGCGCCGCCTGCTGACGTCGATGGCCGAG
CTGTTCGTCCGCGGTGTTCGCGTCGACTGGGCCACGCTGGTGCCGCCCGCGCGCGTGGAC
CTCCCGACGTACGCCTTCGACCACCAGCACTTCTGGCTCCGGCCGGCCGCGCAGGCGGAC
GCCGTCTCGCTCGGCCAGGCCGCGGCGGAGCACCCGCTGCTCGGCGCGGTCGTCCGGCTG
CCGCAGTCGGACGGCCTGGTCTTCACCTCGCGGCTGTCGCTGCGGACGCACCCGTGGCTG
GCCGACCACACCATCGGCGGCGTGGTGCTGTTCCCCGGCACCGGGCTGGTCGAACTGGCC
GTGCGGGCCGGCGACGAGGCCGGGTGCCCGGTCCTGGACGAACTCGTGACCGAGGCGCCG
CTGGTCGTGCCCGGGCAGGGCGGAGTGAACGTCCAGGTCACGGTGAGCGGCCCGGACCAG
AACGGCTTGCGCACGGTGGACATCCACTCCCAGCGCGACGACGTGTGGACCCGGCACGCG
ACCGGAACGGTCTCGGCGACCCCGGCGAGCAGCCCCGGCTTCGACTTCACCGCGTGGCCG
CCGCCGGACGGGCAGCGCGTCGAGATCGGCGACTTCTACGCCGACCTCGCCGAGCGCGGG
TACGCGTACGGGCCCTTGTTCCAGGGCGTGCGGGCGGTGTGGCAGCGCGGCGAAGACGTG
TTCGCCGAGGTCGCGCTGCCCGAAGACCGGCGGGAGGACGCCGCCCGGTTCGGCCTGCAC
CCGGCGTTGCTGGACGCGGCCCTGCAGACCGGGACGATCGCCGCGGCCGCGTCCGGTCAG
CCGGGCAAGTCCGTGATGCCGTTCTCGTGGAACCGGCTGGCGCTGCACGCCGTCGGGGCC
GCGGGCCTCCGGGTCCGCGTGGCCCCCGGCGGACCGGACGCGCTGACCGTCGAGGCCGCC
GACGAGACCGGCGCCCCGGTCCTCACCATGGACTCGCTGATCCTGCGTGAAGTCGCCCTC
GACCAGCTGGACACTGCGCGCGCCGGCTCGCTCTACCGGGTGGACTGGACGCCACTGCCC
ACTGTGGACAGTGCGGTGCCCGCTGGTCGGGCCGAGGTGCTGGAAGCTTTCGGCGAGGAG
CCCCTGGACCTGACCGGCCGGGTGCTGGCCGCCCTGCAGGCGTGGCTTTCCGACGCGGCG
GAGGAAGCCCGCCTGGTCGTGGTGACCCGGGGTGCGGTGCCCGCCGGAGACGGTGTGGTG
AGCGATCCGGCGGGTGCCGCGGTGTGGGGCCTGGTCCGGGCCGCGCAGGCGGAGAACCCG
GACCGGTTCGTCCTGCTCGACACCGACGGCGAGGTGCCGCTGGAAGCGGTGCTGGCGACC
GGTGAGCCGCAGCTCGCGCTGCGCGGCACGACGTTCTCGGTGCCCCGGCTCGCCCGCGTC
ACCGAACCGGCGGAAGCCCCGCTGACGTTCCGTCCGGACGGGACGGTCCTGGTCTCCGGC
GCCGGGACGCTGGGTGCGCTCGCCGCCCGCGACCTCGTCACCCGGCACGGCGTCCGGCGG
CTCGTGCTGGCCAGCCGGCGCGGCCGGGCCGCCGAGGGCATCGACGACCTCGTCGCCGAG
CTGACCGGGCACGGCGCCGAAGTGACGGTCGCCGCCTGCGACGTCTCCGACCGCGACCAG
GTGGCGGCGCTGCTCAAGGAACACGCGCTGACCGCGGTGGTGCACACGGCGGGCGTGTTC
GACGCCGGTGTCACCGGCGCGCTGACCCGGGAGCGGCTGGCCAAGGTGTTCGCGCCCAAG
GTCGACGCGGCCAACCACCTCGACGAGCTGACCCGCGACCTGGACCTCGACGCGTTCATC
GTCTACTCGTCCGCCTCCTCGATCTTCATGGGCGCGGGCAGCGGCGGGTACGCGGCGGCG
AACGCCTACCTCGACGGCCTGATGGCCGCCCGGCGCGCGGCGGGCCTGCCGGGGCTGTCG
CTGGCCTGGGGCCCGTGGGAGCAGCTCACCGGCATGGCCGACACCATCGACGACCTCACC
CTGGCCCGGATGAGCCGGCGCGAAGGCCGCGGCGGCGTCCGCGCGCTCGGCTCCGCCGAC
GGCATGGAGCTGTTCGACGCCGCGCTCGCGGCCGGGCAGGCGCTGCTGGTGCCGATCGAG
CTCGACCTGCGCGAGGTGCGGGCCGACGCGGCCGGCGGCGGCACGGTGCCGCACCTGCTG
CGCGGGCTGGTCCGCGCGGGCCGGCAGGCGGCGCGGACGGCGGCCACCGAGGACGGCGGC
CTGGAACGCCGGCTGGCCGGGCTCACCGTGGCCGAACAGGAAGCGCTGCTGCTCGACCTC
GTCCGCGGTCAGGTCGCCGTCGTGCTCGGGCACGCCGACAGCTCCGGCGTCCGCGCCGAC
GCGGCGTTCAAGGACGCCGGGTTCGACTCGCTGACGTCGGTGGAGCTGCGCAACCGGCTG
CGCGAGACGACCGGCCTGAAACTGCCCGCGACGCTGGTCTTCGACCATCCGAACCCGCTG
GCACTGGCCCGGCACCTGCGGGCGGAACTCGCCGTCGACGAGGCATCCCCGGCCGATGCG
GTGCTGGCCGGGCTCGCCGGGCTGGAGGCGGCCATCGCGGCCGCCGGCGCCCCGGACGGC
GACCGGATCACCGCGCGGCTGCGGGAACTGCTCAAGGCCGCCGAGGCGGCCGAGGCCCGG
CCGGGCACCTCCGGCGATCTCGACACGGCCAGCGACGAGGAACTGTTCGCCCTCGTCGAC
GGGCTCGACTGA

[7] KS	36..408

[7] AT	555..868

[7] methylmalonyl-CoA	744..748

[7] dh	911..1070

[7] KR	1334..1509

[7] ACP	1617..1687

[7] KS	106..1224

[7] AT	1663..2604

[7] methylmalonyl-CoA	2230..2244

[7] dh	2731..3210

[7] KR	4000..4527

[7] ACP	4849..5061

Feature

BLASTP Database:UniProtKB:2011_09	show BLAST table
InterPro Database:interpro:38.0	IPR001227 Acyl transferase domain (Domain) G3DSA:3.40.366.10 no description IPR006162 Phosphopantetheine attachment site (PTM) PS00012 PHOSPHOPANTETHEINE IPR009081 Acyl carrier protein-like (Domain) G3DSA:1.10.1200.10 no description PS50075 ACP_DOMAIN SSF47336 ACP-like PF00550 PP-binding IPR013968 Polyketide synthase, KR (Domain) PF08659 KR IPR014030 Beta-ketoacyl synthase, N-terminal (Domain) PF00109 ketoacyl-synt IPR014031 Beta-ketoacyl synthase, C-terminal (Domain) PF02801 Ketoacyl-synt_C IPR014043 Acyl transferase (Domain) PF00698 Acyl_transf_1 IPR016035 Acyl transferase/acyl hydrolase/lysophospholipase (Domain) SSF52151 FabD/lysophospholipase-like IPR016036 Malonyl-CoA ACP transacylase, ACP-binding (Domain) SSF55048 Probable ACP-binding domain of malonyl-CoA ACP transacylase IPR016038 Thiolase-like, subgroup (Domain) G3DSA:3.40.47.10 no description IPR016039 Thiolase-like (Domain) SSF53901 Thiolase-like IPR016040 NAD(P)-binding domain (Domain) G3DSA:3.40.50.720 no description IPR018201 Beta-ketoacyl synthase, active site (Active_site) PS00606 B_KETOACYL_SYNTHASE IPR020801 Polyketide synthase, acyl transferase domain (Domain) SM00827 Acyl transferase domain in polyketide syntha IPR020806 Polyketide synthase, phosphopantetheine-binding domain (Domain) SM00823 Phosphopantetheine attachment site IPR020807 Polyketide synthase, dehydratase domain (Domain) SM00826 no description IPR020841 Polyketide synthase, beta-ketoacyl synthase domain (Domain) SM00825 Beta-ketoacyl synthase IPR020842 Polyketide synthase/Fatty acid synthase, KR (Domain) SM00822 no description
SignalP	No significant hit
TMHMM	No significant hit

Rifam_00220 Rifam_00240