ISDA

Deposition Date 2005-06-10

Release Date 2005-09-13

Last Version Date 2024-11-20

Entry Detail

PDB ID:

1ZYR

Keywords:

TRANSCRIPTION,TRANSFERASE

Title:

Structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 274)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.00 Å

R-Value Free:

0.28

R-Value Work:

0.26

Space Group:

P 32

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase alpha chain
Gene (Uniprot):rpoA
Chain IDs:A, B, G (auth: K), H (auth: L)
Chain Length:315
Number of Molecules:4
Biological Source:Thermus thermophilus

UniProt ID:Q5SHR6 Pfam ID:PF01193, PF01000, PF03118 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase beta chain
Gene (Uniprot):rpoB
Chain IDs:C, I (auth: M)
Chain Length:1119
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q8RQE9 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
Gene (Uniprot):rpoC
Chain IDs:D, J (auth: N)
Chain Length:1524
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q8RQE8 Pfam ID:PF04997, PF21668, PF00623, PF04983, PF05000, PF04998 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase omega chain
Gene (Uniprot):rpoZ
Chain IDs:E, K (auth: O)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q8RQE7 Pfam ID:PF01192 EC:2.7.7.6

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase sigma chain
Gene (Uniprot):sigA
Chain IDs:F, L (auth: P)
Chain Length:423
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SKW1 Pfam ID:PF00140, PF04542, PF04539, PF04545

Ligand Molecules

STD

Primary Citation

Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.

Tuske, S, Sarafianos, S.G, Wang, X, Hudson, B, Sineva, E, Mukhopadhyay, J, Birktoft, J.J, Leroy, O, Ismail, S, Clark, A.D, Dharia, C, Napoli, A, Laptenko, O, Lee, J, Borukhov, S, Ebright, R.H, Arnold, E.Show

Cell(Cambridge,Mass.) 122 541 552 (2005)

PMID: 16122422 DOI: 10.1016/j.cell.2005.07.017

Abstact

We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight-bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents.

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Primary Citation of related structures