PDBsum entry 3wod

Transferase/transcription

PDB id: 3wod

Contents

Protein chains

225 a.a.

1118 a.a.

1488 a.a.

95 a.a.

278 a.a.

127 a.a.

91 a.a.

Metals

_ZN

PDB id:

3wod

Name:

Transferase/transcription

Title:

RNA polymerase-gp39 complex

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b. Synonym: rnap subunit alpha, RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c. Synonym: rnap subunit beta, RNA polymerase subunit beta, transcriptase subunit beta. DNA-directed RNA polymerase subunit beta'.

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Thermus phage p23-45. Organism_taxid: 466051. Gene: gp39, p23p39. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.60Å R-factor: 0.251 R-free: 0.279

Authors:

S.Tagami,S.Sekine,L.Minakhin,D.Esyunina,R.Akasaka,M.Shirouzu, A.Kulbachinskiy,K.Severinov,S.Yokoyama

Key ref:

S.Tagami et al. (2014). Structural basis for promoter specificity switching of RNA polymerase by a phage factor. Genes Dev, 28, 521-531. PubMed id: 24589779 DOI: 10.1101/gad.233916.113

Date:

26-Dec-13 Release date: 12-Mar-14

Protein chains

Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 315 a.a.

Struc: 225 a.a.

Protein chain

Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1119 a.a.

Struc: 1118 a.a.

Protein chain

Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta' from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1524 a.a.

Struc: 1488 a.a.

Protein chain

Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 99 a.a.

Struc: 95 a.a.*

Protein chain

Q5SKW1  (Q5SKW1_THET8) -  RNA polymerase sigma factor SigA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 423 a.a.

Struc: 278 a.a.

Protein chain

A7XX65  (A7XX65_BP234) -  Uncharacterized protein from Thermus virus P23-45

Seq: 141 a.a.

Struc: 127 a.a.

Protein chain

A7XX65  (A7XX65_BP234) -  Uncharacterized protein from Thermus virus P23-45

Seq: 141 a.a.

Struc: 91 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1101/gad.233916.113

Genes Dev 28:521-531 (2014)

PubMed id: 24589779

Structural basis for promoter specificity switching of RNA polymerase by a phage factor.

S.Tagami, S.Sekine, L.Minakhin, D.Esyunina, R.Akasaka, M.Shirouzu, A.Kulbachinskiy, K.Severinov, S.Yokoyama.

ABSTRACT

Transcription of DNA to RNA by DNA-dependent RNA polymerase (RNAP) is the first step of gene expression and a major regulation point. Bacteriophages hijack their host's transcription machinery and direct it to serve their needs. The gp39 protein encoded by Thermus thermophilus phage P23-45 binds the host's RNAP and inhibits transcription initiation from its major "-10/-35" class promoters. Phage promoters belonging to the minor "extended -10" class are minimally inhibited. We report the crystal structure of the T. thermophilus RNAP holoenzyme complexed with gp39, which explains the mechanism for RNAP promoter specificity switching. gp39 simultaneously binds to the RNAP β-flap domain and the C-terminal domain of the σ subunit (region 4 of the σ subunit [σ4]), thus relocating the β-flap tip and σ4. The ~45 Å displacement of σ4 is incompatible with its binding to the -35 promoter consensus element, thus accounting for the inhibition of transcription from -10/-35 class promoters. In contrast, this conformational change is compatible with the recognition of extended -10 class promoters. These results provide the structural bases for the conformational modulation of the host's RNAP promoter specificity to switch gene expression toward supporting phage development for gp39 and, potentially, other phage proteins, such as T4 AsiA.