Rifam_00420 : CDS information

Location

Organism	Amycolatopsis mediterranei
Strain	S699
Entry name	Rifamycin
Contig	AF040570
Start / Stop / Direction	85,208 / 83,901 / - [in whole cluster] 85,208 / 83,901 / - [in contig]
Location	complement(83901..85208) [in whole cluster] complement(83901..85208) [in contig]
Type	CDS
Length	1,308 bp (435 aa)

Annotation

Category	5.1 general function
Product	putative pyridoxamine 5'-phosphate-dependent NDP-hexose C-3 dehydratase
Product (GenBank)	putative dNTP-hexose dehydratase
Gene
Gene (GenBank)
EC number
Keyword
Note
Note (GenBank)	ORF6
Reference	ACC O52562 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) comment ansamycin系抗生物質rifamycinの生合成gene clusterの報告。 Orf6(435aa): dNTP-hexose dehydrogenase orf6-10はamino-deoxyhexose nucleotide形成をコードするgenesのようで、Orf6にはdeoxyhexose nucleotideのreductive 3-deoxygenationが想定される。しかしこれまでにA. mediterranei S699ではglycosylateされたrifamycinは報告されていないのでsilent geneかもしれない。これに一致して、orf6, orf9の不活化はrifamycin B産生に影響しない。 Streptomyces tolypophorusではglycosylated rifamycin derivativesであるtolypomycinsが分離されており、この菌はrifamycin Bも産生する。tolypomycinsのC4に付加する糖4-amino-2,3-dideoxy-L-rhamnoseの生合成後期段階には、orf6-10によってコードされるような酵素を必要とする。
Related Reference	ACC Q9L4S6 NITE Urd_00240 PmId [11094336] The NDP-sugar co-substrate concentration and the enzyme expression level influence the substrate specificity of glycosyltransferases: cloning and characterization of deoxysugar biosynthetic genes of the urdamycin biosynthetic gene cluster. (Chem Biol. , 2000) [17434221] Surprising production of a new urdamycin derivative by S. fradiae Delta urdQ/R. (J Biotechnol. , 2007) comment 3rd(Q9L4S6) 71%, 0.0 Streptomyces fradiae_urdQ NDP-hexose 3,4-dehydratase UrdQ --- [PMID: 11094336](2000) urdZ3, urdQ and urdZ1をそれぞれ不活化するとL-rhodinoseを産生できない株となり、主にurdamycinone B (D-olivoseあり、L-rhodinoseなし)を蓄積。各genesで相補され、urdamycin A産生回復。よってこれらのgenesはNDP-L-rhodinose生合成にのみ関与する。 urdamycin deoxysugar(NDP-D-olivose, NDP-L-rhodinose)生合成経路のFigあり。 UrdQ = NDP-4-keto-2,6-dideoxy-D-glucose → NDP-D-cinerulose この機能的割り当てを確認するにはさらなる研究が必要。 --- [PMID: 17434221](2007) urdQ/R double mutantの相補実験あり。 S. cyanogenus S136に由来するlandomycin生合成gene clusterの dTDP-hexose-3,4-dehydrataseをコードするlanQと、 dTDP-hexose-4-ketoreductaseをコードするlanRでの相補は、 urdamycin A and urdamycin Bの産生をもたらした。ただ、lanQ,lanR自体が機能確認されていないようなので微妙。
Related Reference	ACC Q9ALN8 NITE Spino_00050 PmId [17076492] Characterization of SpnQ from the spinosyn biosynthetic pathway of Saccharopolyspora spinosa: mechanistic and evolutionary implications for C-3 deoxygenation in deoxysugar biosynthesis. (J Am Chem Soc. , 2006) [18345667] In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. (J Am Chem Soc. , 2008) comment 21st, id66%, 1e-154 Saccharopolyspora spinosa_spnQ probable NDP-hexose-3,4-dehydratase [Spino_00050]pyridoxamine 5'-phosphate-dependent NDP-hexose C-3 dehydratase forosamine生合成におけるC-3 deoxygenationに関与したPMP-dependent 3-dehydratase --- [PMID: 17076492](2006) SpnQをクローニング、過剰発現、精製して、"ColD-like" conditions と "E1-like" conditionsの両方で触媒活性をテスト。 E3のような特異的reductaseを必要とせず、一般的なferredoxin/ferredoxin reductase またはflavodoxin/flavodoxin reductaseと効率的に働く。 --- [PMID: 18345667](2008) dTDP-D-forosamine形成に関連する5つの酵素SpnO, N, Q, R, and Sの生化学的機能解明。使用している株はNRRL 18537. SpnQのsteady-state kinetic parameters、基質特異性を調査。

Sequence

>putative pyridoxamine 5'-phosphate-dependent NDP-hexose C-3 dehydratase [putative dNTP-hexose dehydratase]
MVDSARSDLLTQVRDYHDAQSPGPAPFIPGQTPILSSGAVLDAADREALVAAALDLRIAS
GTIATKFESSFARKLKRRKAVLTNSGSSANLLALSTLTSPTLGDEQLKPGDEVVTVAAGF
PTTVNPILQNGMIPVFVDIELGTYNTTAERVEAAISPRTRAIMIAHTLGNPFPVAEIAEI
AQRHGCHLIEDNCDAVGSTYQGQLTGTFGRFSTVSFYPAHHLTMGEGGMLLSSDIKLAKL
AKSFRDWGRDCWCEPGEDDRCLKRFDLHLGTLPEAYDHKYVFSEVGYNLKSTDIHAALGL
SQLAKLPDFVDARKRNWRQLREGLDGLPGLILPEATPGSDPSWFGFIITVKPDAGFDVPE
VVEYLEARNIRTRRLFAGNLTRHPAYIGKPQRIAGPLTNSDIVTERTFWIGVYPGITTEM
IEYVIGTLKEFVATH

>putative pyridoxamine 5'-phosphate-dependent NDP-hexose C-3 dehydratase [putative dNTP-hexose dehydratase]
ATGGTCGACTCAGCCCGATCGGACCTGCTGACGCAGGTTCGCGACTACCACGACGCCCAG
TCCCCCGGGCCGGCGCCGTTCATCCCGGGGCAGACACCGATCCTGTCGTCCGGGGCGGTG
CTGGACGCCGCCGACCGCGAAGCCCTGGTGGCCGCCGCGCTCGACCTGCGCATCGCCTCC
GGCACCATCGCGACGAAGTTCGAGTCGTCCTTCGCCCGGAAACTCAAGCGGCGCAAGGCG
GTGCTGACGAACTCCGGCTCGTCGGCGAACCTGCTGGCGCTGAGCACGCTGACGTCCCCG
ACGCTGGGCGACGAGCAGCTCAAGCCGGGCGACGAGGTCGTCACGGTCGCGGCCGGCTTC
CCGACCACGGTGAACCCGATCCTGCAGAACGGCATGATCCCGGTGTTCGTCGACATCGAG
CTCGGCACGTACAACACGACCGCCGAACGGGTCGAAGCGGCGATCTCCCCGCGCACGCGC
GCCATCATGATCGCCCACACGCTGGGAAATCCTTTCCCGGTGGCGGAAATCGCCGAAATC
GCCCAGCGCCACGGCTGCCACCTCATCGAGGACAACTGCGACGCCGTCGGCTCCACCTAC
CAGGGACAGCTCACCGGCACGTTCGGCCGGTTCTCGACGGTGTCCTTCTACCCAGCCCAC
CACCTGACCATGGGCGAGGGCGGCATGCTGCTGTCCTCGGACATCAAGCTGGCCAAGCTG
GCGAAGTCGTTCCGCGACTGGGGCCGCGACTGCTGGTGCGAGCCCGGCGAGGACGACCGC
TGCCTGAAGCGGTTCGACCTGCACCTCGGCACGCTGCCGGAGGCCTACGACCACAAGTAC
GTCTTCTCCGAGGTCGGCTACAACCTCAAGAGCACCGACATCCACGCCGCGCTCGGGCTG
AGCCAGCTGGCGAAACTGCCGGACTTCGTCGACGCCCGCAAGCGCAACTGGCGTCAGCTG
CGCGAAGGCCTCGACGGCCTGCCCGGGCTGATCCTGCCGGAGGCCACGCCGGGCAGCGAC
CCGAGCTGGTTCGGGTTCATCATCACGGTGAAACCCGACGCCGGCTTCGACGTCCCGGAG
GTCGTCGAGTACCTCGAGGCGCGCAACATCCGCACCCGGCGGCTGTTCGCGGGCAACCTG
ACCCGCCACCCCGCCTACATCGGCAAGCCGCAGCGCATCGCCGGCCCGCTGACCAACAGC
GACATCGTCACCGAGCGGACGTTCTGGATCGGCGTCTACCCGGGGATCACCACGGAGATG
ATCGAGTACGTGATCGGCACGCTCAAGGAGTTCGTCGCCACGCACTGA

Feature

BLASTP Database:UniProtKB:2011_09	show BLAST table
InterPro Database:interpro:38.0	IPR000653 DegT/DnrJ/EryC1/StrS aminotransferase (Family) PF01041 DegT_DnrJ_EryC1 IPR015421 Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (Domain) G3DSA:3.40.640.10 no description IPR015422 Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (Domain) G3DSA:3.90.1150.10 no description IPR015424 Pyridoxal phosphate-dependent transferase, major domain (Domain) SSF53383 PLP-dependent transferases
SignalP	No significant hit
TMHMM	No significant hit

Rifam_00410 Rifam_00430