ISDA

Deposition Date 2017-01-11

Release Date 2017-04-12

Last Version Date 2024-10-30

Entry Detail

PDB ID:

5UH8

Keywords:

TRANSCRIPTION/DNA/RNA

Title:

Crystal structure of Mycobacterium tuberculosis transcription initiation complex containing 4nt RNA

Biological Source:

Source Organism:

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (Taxon ID: 83332)

Host Organism:

Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

4.18 Å

R-Value Free:

0.25

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit alpha
Gene (Uniprot):rpoA
Chain IDs:A, B
Chain Length:347
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WGZ1 Pfam ID:PF01193, PF01000, PF03118 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):rpoB
Chain IDs:C
Chain Length:1178
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WGY9 Pfam ID:PF04563, PF04561, PF04565, PF10385, PF00562, PF04560 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta'
Chain IDs:D
Chain Length:1316
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WGY7 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit omega
Gene (Uniprot):rpoZ
Chain IDs:E
Chain Length:110
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WGY5 Pfam ID:PF01192 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RNA polymerase sigma factor SigA
Gene (Uniprot):sigA
Chain IDs:F
Chain Length:528
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

UniProt ID:P9WGI1 Pfam ID:PF00140, PF04542, PF04539, PF04545 EC:2.7.7.6

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*G)-3')
Chain IDs:H (auth: G)
Chain Length:16
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*G)-3')
Chain IDs:G (auth: H)
Chain Length:23
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*UP*CP*GP*A)-3')
Chain IDs:I
Chain Length:4
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Ligand Molecules

Primary Citation

Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.

Lin, W, Mandal, S, Degen, D, Liu, Y, Ebright, Y.W, Li, S, Feng, Y, Zhang, Y, Mandal, S, Jiang, Y, Liu, S, Gigliotti, M, Talaue, M, Connell, N, Das, K, Arnold, E, Ebright, R.H.Show

Mol. Cell 66 169 179.e8 (2017)

PMID: 28392175 DOI: 10.1016/j.molcel.2017.03.001

Abstact

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif, at 3.8-4.4 Å resolution. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report non-Rif-related compounds-Nα-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.

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Primary Citation of related structures