PDBsum entry 4g7z

Transcription, transferase/DNA

PDB id: 4g7z

Contents

Protein chains

226 a.a.

1111 a.a.

1482 a.a.

94 a.a.

346 a.a.

DNA/RNA

Metals

_MG ×2

_ZN ×4

PDB id:

4g7z

Name:

Transcription, transferase/DNA

Title:

Crystal structure of thermus thermophilus transcription initiation complex containing 5-bru at template-strand position +1

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b, k, l. Synonym: rnap subunit alpha, RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c, m. 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. Gene: rpod, ttha0532. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes

Resolution:

3.82Å R-factor: 0.177 R-free: 0.232

Authors:

Y.Zhang,R.H.Ebright

Key ref:

Y.Zhang et al. (2012). Structural basis of transcription initiation. Science, 338, 1076-1080. PubMed id: 23086998

Date:

20-Jul-12 Release date: 31-Oct-12

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: 226 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: 1482 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.

DNA/RNA chains

T-A-T-A-A-T-G-G-G-A-G-C-T-G-T-C-A-C-G-G-A-T-G-C 24 bases

G-C-A-T-C-C-G-T-G-A-G-BRU-C-G-A-G 16 bases

T-A-T-A-A-T-G-G-G-A-G-C-T-G-T-C-A-C-G-G-A-T-G-C 24 bases

G-C-A-T-C-C-G-T-G-A-G-BRU-C-G-A-G 16 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, K, L, M, N, O: 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

Science 338:1076-1080 (2012)

PubMed id: 23086998

Structural basis of transcription initiation.

Y.Zhang, Y.Feng, S.Chatterjee, S.Tuske, M.X.Ho, E.Arnold, R.H.Ebright.

ABSTRACT

During transcription initiation, RNA polymerase (RNAP) binds and unwinds promoter DNA to form an RNAP-promoter open complex. We have determined crystal structures at 2.9 and 3.0 Å resolution of functional transcription initiation complexes comprising Thermus thermophilus RNA polymerase, σ(A), and a promoter DNA fragment corresponding to the transcription bubble and downstream double-stranded DNA of the RNAP-promoter open complex. The structures show that σ recognizes the -10 element and discriminator element through interactions that include the unstacking and insertion into pockets of three DNA bases and that RNAP recognizes the -4/+2 region through interactions that include the unstacking and insertion into a pocket of the +2 base. The structures further show that interactions between σ and template-strand single-stranded DNA (ssDNA) preorganize template-strand ssDNA to engage the RNAP active center.