PDBsum entry 5i2d

Transcription/DNA/RNA

PDB id: 5i2d

Contents

Protein chains

284 a.a.

1111 a.a.

1363 a.a.

94 a.a.

346 a.a.

195 a.a.

DNA/RNA

Metals

_MG ×2

_ZN ×4

PDB id:

5i2d

Name:

Transcription/DNA/RNA

Title:

Crystal structure of t. Thermophilus tthb099 class ii transcription activation complex: tap-rpo

Structure:

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

Source:

Thermus thermophilus (strain hb8 / atcc 27634 / dsm 579). Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Gene: siga, ttha0532. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: tthb099. Synthetic: yes.

Resolution:

4.41Å R-factor: 0.243 R-free: 0.284

Authors:

Y.Feng,Y.Zhang,R.H.Ebright

Key ref:

Y.Feng et al. (2016). Structural basis of transcription activation. Science, 352, 1330-1333. PubMed id: 27284196 DOI: 10.1126/science.aaf4417

Date:

08-Feb-16 Release date: 22-Jun-16

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: 284 a.a.

Protein chains

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

Seq: 1119 a.a.

Struc: 1111 a.a.

Protein chains

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

Seq: 1524 a.a.

Struc: 1363 a.a.

Protein chains

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

Seq: 99 a.a.

Struc: 94 a.a.

Protein chains

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

Seq: 423 a.a.

Struc: 346 a.a.

Protein chains

Q53W63  (LDRP_THET8) -  Transcriptional regulator LdrP from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 195 a.a.

Struc: 195 a.a.

DNA/RNA chains

G-C-C-C-T-T-G-T-G-A-G-C-C-A-C-C-T-C-A-C-A-G-T-C-A-A-G-G-C-C-C-G-T-C-C-G-T-T-G- 66 bases

G-C-A-T-C-C-G-T-G-A-G-T-C-G-A-G-G-G-T-A-A-T-A-A-C-G-G-C-A-A-C-G-G-A-C-G-G-G-C- 66 bases

U-C-G-A 4 bases

G-C-C-C-T-T-G-T-G-A-G-C-C-A-C-C-T-C-A-C-A-G-T-C-A-A-G-G-C-C-C-G-T-C-C-G-T-T-G- 66 bases

G-C-A-T-C-C-G-T-G-A-G-T-C-G-A-G-G-G-T-A-A-T-A-A-C-G-G-C-A-A-C-G-G-A-C-G-G-G-C- 66 bases

U-C-G-A 4 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, L, M, N, O, P: 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: 10.1126/science.aaf4417

Science 352:1330-1333 (2016)

PubMed id: 27284196

Structural basis of transcription activation.

Y.Feng, Y.Zhang, R.H.Ebright.

ABSTRACT

Class II transcription activators function by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initial RNA polymerase (RNAP)-promoter closed complex into a catalytically competent RNAP-promoter open complex. Here, we report a 4.4 angstrom crystal structure of an intact bacterial class II transcription activation complex. The structure comprises Thermus thermophilus transcription activator protein TTHB099 (TAP) [homolog of Escherichia coli catabolite activator protein (CAP)], T. thermophilus RNAP σ(A) holoenzyme, a class II TAP-dependent promoter, and a ribotetranucleotide primer. The structure reveals the interactions between RNAP holoenzyme and DNA responsible for transcription initiation and reveals the interactions between TAP and RNAP holoenzyme responsible for transcription activation. The structure indicates that TAP stimulates isomerization through simple, adhesive, stabilizing protein-protein interactions with RNAP holoenzyme.