Rifam_00620 Rifam_00620   Rifam_00640 Rifam_00640

Rifam_00630 : CDS information

close this sectionLocation

Organism
StrainS699
Entry nameRifamycin
Contig
Start / Stop / Direction105,773 / 109,276 / + [in whole cluster]
105,773 / 109,276 / + [in contig]
Location105773..109276 [in whole cluster]
105773..109276 [in contig]
TypeCDS
Length3,504 bp (1,167 aa)
Click on the icon to see Genetic map.

close this sectionAnnotation

Category4.4 resistance
Productputative rifamycin-resistant DNA-directed RNA polymerase subunit beta
Product (GenBank)RpoB
Gene
Gene (GenBank)rpoB
EC number2.7.7.6
Keyword
Note
Note (GenBank)
  • DNA-dependent RNA polymerase beta-subunit
Reference
ACC
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)
[16079331] Identification of tailoring genes involved in the modification of the polyketide backbone of rifamycin B by Amycolatopsis mediterranei S699. (Microbiology. , 2005)
comment
[PMID: 9512878](1998)
未発表知見を引用したコメントのみ。
自身の抗生物質に対する抵抗性メカニズムのうち、target siteや二次代謝産物の修飾に関連するタイプの例としてrpoBを挙げている。

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[PMID: 16079331](2005)
fig2のschemaなどplasmid作成に関して記述はあるが、各ORFの詳細は不明。
Related Reference
ACC
P0A680
PmId
[8031050] The rpoB gene of Mycobacterium tuberculosis. (Antimicrob Agents Chemother. , 1994)
[21704562] Rifamycin inhibition of WT and Rif-resistant Mycobacterium tuberculosis and Escherichia coli RNA polymerases in vitro. (Tuberculosis (Edinb). , 2011)
comment
51st, 82%, 0.0
Mycobacterium tuberculosis_rpoB
DNA-directed RNA polymerase subunit beta(EC 2.7.7.6)

rifamycin SVから合成されたrifampicinは抗結核薬として使用されているが、耐性菌の出現が早いことが問題点である。耐性はRNA polymeraseの突然変異による。

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[PMID:8031050](1994)
RNA polymeraseのbeta subunitをコードするrpoBC部分の分離。
E.coli rpoBC operonに似た構成。

M. tuberculosis H37Rvのrifampin感受性株からクローニングしたrpoBを、rifampin抵抗性のあるM. smegmatis LR223株に導入するとrifampin感受性になった。
また、456番目の残基をserine(TCG)→leucine(TTG)に変更したM. tuberculosis rpoBを、rifampinに感受性のあるM. smegmatis LR222株に導入するとrifampin抵抗性を示した。

---
[PMID:21704562](2011)
M. tuberculosis Rifamycin抵抗性臨床株はbeta-Asp435, beta-His445, and beta-Ser450のどれかに変異があることがほとんど。

---
rifamycin cluster RpoBでこれらに相当する残基は、
441 D → 432Q
451 H → 442H
456 S → 447N

変異あり。よってこのRpoBもrifamycin抵抗性がありそう。
M. tuberculosisのRifamycin抵抗性に関する論文は他にもいくつかある。
Family/Domain
FD
IPR010243
comment
[IPR010243] DNA-directed RNA polymerase, beta subunit (Family)
function: DNA-directed RNA polymerase activity, DNA binding

close this sectionSequence

selected fasta
>putative rifamycin-resistant DNA-directed RNA polymerase subunit beta [RpoB]
MAVSPANQATAATTSAESRSEATGIPGAPKRVSFAKIREPLNTPNLLDVQIQSFQWFTGD
EAWFQRRVEEGEENPVGGLEEVLNEISPIEDFSGSMSLSFSAPRFDEVKASIEECKDKDM
TYAAPLFVTAEFVNNNTGEIKSQTVFLGDFPVMTDKGTFVINGTERVVVSQLVRSPGVYY
SKDIDKTSDKDVFSVRVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTTEA
IRERFSFSETLLATLEKDHTAGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKAKRYD
LAKVGRYKVNKKLGLSTPIENGTLTEEDIVTIIEYLVRLHAGEDKMTAANNTEIPVETDD
IDHFGNRRIRTVGELIQNQIRVGLSRTERVVRERMTTQDVEAITPQTLINIRPIGAAIKE
FFGTSQLSQFMQQTNPIDGLTHKRRLNALGPGGLSRERAGMEVRDVHPSHYGRMCPIETP
EGPNIGLIGSLCSYARVNPFGFIETPYRKVVEGRVTDQIDYLTADEEDRFVKAQANAPIS
DDGTFIEDRVMARRKGGEVELIDPLDIDYMDVSPRQMVSIATAMIPFLEHDDANRALMGA
NMQRQAVPLLRSQAPYVGTGVELRAAIDSGDMLVAEQSGVVEELSADLITVMHDDGTRKS
YSLYKFRRSNHGTCFNHRPIVNEGDRIEAGQVIADGPSTENGEVALGKNLLVAVMPWEGH
NYEDAIILSERLVQDDVLTSIHIEEHEIDARDTKLGAEEITRDIPNVSEEVLADLDERGI
IRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGETGKVIG
IRVFSREDDDELPPGVNELVRVYVAQKRKIQPGDKLAGRHGNKGVIGKILPVEDMPFMED
GTPVDIILNTHGVPRRMNIGQILELHLGWLASQGWTIEGDPDWAKNLSAELRDVAPGTNT
ATPVFDGAKEEELTGLLSATKPNRDGERMVKENGKANLFDGRSGEPYPYPVAVGYMYILK
LHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIK
SDDVVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGSSIEMRDSGD
EDLERAAANLGINLSRNESPSVDDVVH
selected fasta
>putative rifamycin-resistant DNA-directed RNA polymerase subunit beta [RpoB]
TTGGCAGTCTCTCCCGCGAACCAGGCCACTGCTGCGACCACCTCGGCTGAATCTCGCTCG
GAGGCCACGGGAATCCCCGGCGCGCCCAAGCGGGTTTCCTTCGCAAAGATTCGCGAACCC
CTGAACACCCCCAACCTGCTCGACGTCCAGATCCAGTCGTTCCAGTGGTTCACCGGGGAC
GAAGCGTGGTTCCAGCGCCGTGTCGAGGAAGGTGAAGAGAACCCGGTCGGCGGCCTCGAA
GAGGTCCTCAACGAGATCTCCCCGATCGAAGACTTCTCCGGTTCGATGTCCCTGTCCTTC
TCCGCCCCGCGCTTCGACGAGGTCAAGGCCTCGATCGAGGAGTGCAAGGACAAGGACATG
ACGTACGCGGCCCCGCTGTTCGTCACGGCGGAGTTCGTCAACAACAACACGGGCGAGATC
AAGAGCCAGACGGTCTTCCTGGGCGACTTCCCGGTGATGACCGACAAGGGCACCTTCGTC
ATCAACGGCACCGAGCGTGTCGTGGTGTCCCAGCTGGTCCGCTCGCCGGGCGTCTACTAC
TCCAAGGACATCGACAAGACGAGCGACAAGGACGTCTTCAGCGTCCGCGTCATCCCGAGC
CGCGGTGCCTGGCTGGAGTTCGACGTCGACAAGCGCGACACCGTCGGCGTCCGCATCGAC
CGCAAGCGCCGCCAGCCGGTCACCGTGCTGCTGAAGGCGCTCGGCTGGACCACCGAGGCG
ATCCGCGAGCGCTTCTCCTTCTCGGAGACGCTGCTCGCCACCCTCGAGAAGGACCACACC
GCCGGCACCGACGAGGCGCTGCTCGACATCTACCGCAAGCTCCGCCCGGGCGAACCGCCC
ACCAAGGAGAGCGCGCAGACCCTGCTGGAGAACCTGTTCTTCAAGGCGAAGCGCTACGAC
CTGGCCAAGGTCGGCCGGTACAAGGTCAACAAGAAGCTGGGCCTCTCGACCCCGATCGAG
AACGGCACGCTGACCGAAGAGGACATCGTCACGATCATCGAGTACCTGGTCCGGCTGCAC
GCCGGCGAGGACAAGATGACCGCGGCGAACAACACCGAGATCCCGGTCGAGACCGACGAC
ATCGACCACTTCGGCAACCGCCGGATCCGGACCGTCGGCGAGCTGATCCAGAACCAGATC
CGGGTCGGCCTGTCGCGCACTGAGCGCGTCGTCCGCGAGCGCATGACCACGCAGGACGTC
GAGGCGATCACCCCGCAGACCCTGATCAACATCCGCCCGATCGGCGCGGCGATCAAGGAG
TTCTTCGGCACCTCGCAGCTGTCGCAGTTCATGCAGCAGACGAACCCGATCGACGGCCTG
ACCCACAAGCGCCGCCTCAACGCGCTGGGCCCGGGTGGTCTGTCGCGTGAGCGCGCCGGC
ATGGAGGTCCGCGACGTCCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAGACGCCG
GAAGGCCCGAACATCGGCCTGATCGGCTCGCTCTGCTCCTACGCGCGGGTCAACCCGTTC
GGCTTCATCGAGACGCCGTACCGCAAGGTCGTCGAGGGCCGGGTCACCGACCAGATCGAC
TACCTGACCGCGGACGAAGAAGACCGGTTCGTCAAGGCCCAGGCCAACGCGCCGATCTCG
GACGACGGCACCTTCATCGAAGACCGGGTCATGGCCCGCCGCAAGGGCGGCGAGGTCGAG
CTGATCGACCCGCTCGACATCGACTACATGGACGTGTCGCCGCGGCAGATGGTCTCGATC
GCGACGGCGATGATCCCGTTCCTCGAGCACGACGACGCGAACCGCGCGCTGATGGGCGCG
AACATGCAGCGTCAGGCCGTGCCGCTGCTGCGCAGCCAGGCGCCGTACGTCGGCACCGGC
GTGGAGCTGCGGGCCGCGATCGACTCCGGCGACATGCTGGTCGCCGAGCAGTCGGGCGTG
GTGGAGGAGCTGTCGGCGGACCTGATCACGGTCATGCACGACGACGGCACGCGGAAGAGC
TACAGCCTCTACAAGTTCCGCCGCTCGAACCACGGCACCTGCTTCAACCACCGCCCGATC
GTCAACGAGGGCGACCGGATCGAAGCGGGCCAGGTCATCGCCGACGGCCCGTCCACCGAA
AACGGTGAGGTGGCGCTCGGCAAGAACCTGCTGGTCGCGGTCATGCCGTGGGAGGGCCAC
AACTACGAGGACGCGATCATCCTCTCCGAGCGCCTGGTGCAGGACGACGTGCTGACGTCG
ATCCACATCGAGGAGCACGAGATCGATGCCCGCGACACGAAGCTGGGCGCCGAGGAGATC
ACCCGGGACATCCCGAACGTCTCCGAAGAAGTCCTGGCCGACCTCGACGAGCGCGGCATC
ATCCGGATCGGTGCCGAGGTCCGCGACGGCGACATCCTGGTCGGCAAGGTCACGCCGAAG
GGCGAGACCGAGCTGACCCCGGAGGAGCGCCTGCTCCGCGCGATCTTCGGCGAGAAGGCC
CGCGAGGTCCGCGACACCTCCCTGAAGGTGCCGCACGGCGAGACCGGCAAGGTCATCGGC
ATCCGGGTGTTCTCCCGCGAGGACGACGACGAGCTGCCCCCGGGCGTCAACGAGCTGGTC
CGCGTCTACGTGGCCCAGAAGCGCAAGATCCAGCCGGGCGACAAGCTCGCCGGCCGGCAC
GGGAACAAGGGTGTCATCGGCAAGATCCTGCCGGTCGAGGACATGCCGTTCATGGAGGAC
GGCACCCCGGTCGACATCATCCTGAACACCCACGGTGTCCCGCGACGGATGAACATCGGC
CAGATCCTCGAGCTGCACCTGGGCTGGCTGGCGTCGCAGGGCTGGACGATCGAGGGCGAC
CCCGACTGGGCGAAGAACCTGTCGGCCGAGCTCCGCGACGTCGCGCCCGGCACGAACACC
GCCACCCCGGTGTTCGACGGCGCGAAGGAAGAGGAGCTCACCGGGCTGCTCAGCGCGACC
AAGCCGAACCGCGACGGTGAGCGCATGGTCAAGGAGAACGGGAAGGCCAACCTGTTCGAC
GGCCGCTCGGGCGAGCCGTACCCGTACCCGGTCGCGGTCGGCTACATGTACATCCTGAAG
CTGCACCACCTGGTCGACGACAAGATCCACGCCCGCTCCACCGGTCCGTACTCGATGATC
ACGCAGCAGCCGCTGGGTGGTAAGGCGCAGTTCGGTGGCCAGCGCTTCGGTGAGATGGAG
TGCTGGGCGATGCAGGCGTACGGCGCTGCCTACACGCTGCAGGAGCTGCTGACGATCAAG
TCGGACGACGTGGTCGGCCGCGTCAAGGTGTACGAGGCCATCGTCAAGGGGGAGAACATC
CCCGAGCCGGGCATCCCGGAGTCGTTCAAGGTGCTCCTCAAGGAGCTCCAGTCGCTGTGC
CTCAACGTCGAGGTGCTCTCCAGCGACGGCTCCTCGATCGAGATGCGCGACTCCGGCGAC
GAGGACCTCGAGCGCGCCGCGGCGAACCTCGGCATCAACCTGTCCCGCAACGAGTCGCCC
TCGGTGGACGACGTCGTGCACTGA

close this sectionFeature

BLASTP
Database:UniProtKB:2011_09 		show BLAST table
InterPro
Database:interpro:38.0
IPR007120 DNA-directed RNA polymerase, subunit 2, domain 6 (Domain)
[580-1050] 1e-157 PF00562
PF00562   RNA_pol_Rpb2_6
[871-1028] 2e-73 G3DSA:2.40.270.10
G3DSA:2.40.270.10   no description
IPR007121 RNA polymerase, beta subunit, conserved site (Conserved_site)
[873-885] PS01166
PS01166   RNA_POL_BETA
IPR007641 RNA polymerase Rpb2, domain 7 (Domain)
[1052-1126] 5.2e-30 PF04560
PF04560   RNA_pol_Rpb2_7
IPR007642 RNA polymerase Rpb2, domain 2 (Domain)
[174-370] 1.3e-30 PF04561
PF04561   RNA_pol_Rpb2_2
IPR007644 RNA polymerase, beta subunit, protrusion (Domain)
[45-425] 2.8e-28 PF04563
PF04563   RNA_pol_Rpb2_1
IPR007645 RNA polymerase Rpb2, domain 3 (Domain)
[429-498] 2e-26 PF04565
PF04565   RNA_pol_Rpb2_3
IPR010243 DNA-directed RNA polymerase, beta subunit (Family)
[32-1128] 12.245 MF_01321
MF_01321   RNApol_bact_RpoB
[248-847] 9.5e-305 TIGR02013
TIGR02013   rpoB: DNA-directed RNA polymerase, beta subunit
IPR014724 RNA polymerase Rpb2, OB-fold (Domain)
[738-870] 5.3e-57 G3DSA:2.40.50.150
G3DSA:2.40.50.150   no description
IPR019462 DNA-directed RNA polymerase, beta subunit, external 1 domain (Domain)
[508-573] 2e-24 G3DSA:2.30.150.10
G3DSA:2.30.150.10   no description
[507-573] 1.2e-25 PF10385
PF10385   RNA_pol_Rpb2_45
SignalP No significant hit
TMHMM No significant hit
Rifam_00620 Rifam_00620   Rifam_00640 Rifam_00640
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