PDBsum entry 3iyd

Transcription/DNA

PDB id: 3iyd

Contents

Protein chains

322 a.a. *

235 a.a. *

1089 a.a. *

1368 a.a. *

90 a.a. *

479 a.a. *

201 a.a. *

DNA/RNA

Ligands

CMP ×2

* Residue conservation analysis

PDB id:

3iyd

Name:

Transcription/DNA

Title:

Three-dimensional em structure of an intact activator-dependent transcription initiation complex

Structure:

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

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: b3295, jw3257, pez, phs, rpoa, rpob, rpoc, rpod, rpoz, sez. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rpob, gron, nitb, rif, ron, stl, stv, tabd, b3987, jw3950. Synthetic: yes. Other_details: purchased from idt and annealed.

Authors:

B.P.Hudson,J.Quispe,S.Lara,Y.Kim,H.Berman,E.Arnold,R.H.Ebright, C.L.Lawson

Key ref:

B.P.Hudson et al. (2009). Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A, 106, 19830-19835. PubMed id: 19903881 DOI: 10.1073/pnas.0908782106

Date:

01-Aug-09 Release date: 10-Nov-09

Protein chain

P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha from Escherichia coli (strain K12)

Seq: 329 a.a.

Struc: 322 a.a.

Protein chain

P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha from Escherichia coli (strain K12)

Seq: 329 a.a.

Struc: 235 a.a.

Protein chain

P0A8V2  (RPOB_ECOLI) -  DNA-directed RNA polymerase subunit beta from Escherichia coli (strain K12)

Seq: 1342 a.a.

Struc: 1089 a.a.

Protein chain

P0A8T7  (RPOC_ECOLI) -  DNA-directed RNA polymerase subunit beta' from Escherichia coli (strain K12)

Seq: 1407 a.a.

Struc: 1368 a.a.

Protein chain

P0A800  (RPOZ_ECOLI) -  DNA-directed RNA polymerase subunit omega from Escherichia coli (strain K12)

Seq: 91 a.a.

Struc: 90 a.a.

Protein chain

P00579  (RPOD_ECOLI) -  RNA polymerase sigma factor RpoD from Escherichia coli (strain K12)

Seq: 613 a.a.

Struc: 479 a.a.*

Protein chains

P0ACJ8  (CRP_ECOLI) -  DNA-binding transcriptional dual regulator CRP from Escherichia coli (strain K12)

Seq: 210 a.a.

Struc: 201 a.a.

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

DNA/RNA chains

C-G-C-A-A-T-A-A-A-T-G-T-G-A-T-C-T-A-G-A-T-C-A-C-A-T-T-T-T-A-G-G-C-A-A-A-A-A-A- 98 bases

C-T-T-G-T-T-A-T-C-C-G-C-T-C-A-C-A-A-T-T-C-C-A-C-A-C-T-A-A-T-T-A-C-G-A-G-C-C-G- 98 bases

Enzyme reactions

• Enzyme class 2: 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
• Enzyme class 3: Chains F, G, H: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1073/pnas.0908782106

Proc Natl Acad Sci U S A 106:19830-19835 (2009)

PubMed id: 19903881

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.

B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, C.L.Lawson.

ABSTRACT

We present the experimentally determined 3D structure of an intact activator-dependent transcription initiation complex comprising the Escherichia coli catabolite activator protein (CAP), RNA polymerase holoenzyme (RNAP), and a DNA fragment containing positions -78 to +20 of a Class I CAP-dependent promoter with a CAP site at position -61.5 and a premelted transcription bubble. A 20-A electron microscopy reconstruction was obtained by iterative projection-based matching of single particles visualized in carbon-sandwich negative stain and was fitted using atomic coordinate sets for CAP, RNAP, and DNA. The structure defines the organization of a Class I CAP-RNAP-promoter complex and supports previously proposed interactions of CAP with RNAP alpha subunit C-terminal domain (alphaCTD), interactions of alphaCTD with sigma(70) region 4, interactions of CAP and RNAP with promoter DNA, and phased-DNA-bend-dependent partial wrapping of DNA around the complex. The structure also reveals the positions and shapes of species-specific domains within the RNAP beta', beta, and sigma(70) subunits.

Selected figure(s)

Figure 3.
Class I CAP-RNAP-promoter complex EM reconstruction and fitted model: interactions between CAP, αCTD, and σR4 (stereo pair; density contoured at 2.6σ). Coordinates for CAP, αCTD, σR4, and DNA in this region are based on crystal structures of CAP-αCTD-DNA (8) and αCTD-σR4-DNA. CAP activating region 1 (AR1) is shown in yellow; the 287, 265, and 261 determinants of αCTD are shown in green, red, and blue, respectively; and the 596 determinant of σR4 is shown in pink. Ribbon colors are as in Fig. 2. The protomer of αCTD adjacent to CAP has been linked to αNTD^I, but it alternately could have been linked to αNTD^II (alternate linkage position indicated by black sphere at lower right).

Figure 5.
Class I CAP-RNAP-promoter complex EM reconstruction and fitted model: E. coli species-specific RNAP domains. (A) β′ trigger-loop nonconserved domain (β′GNCD) with β′GNCD SBHMa domain in orange; β′GNCD SBMHb domain in yellow; β′ trigger loop in green; β′ jaw in blue (stereo pair). (B) βDR1. (C) βDR2. (D) β residues 1126–1179 (as well as β N-terminal residues 1–9). (E) σ^70NCR with σ^70NCR insert in green and 20-residue negatively charged loop that is disordered in the crystal structure of the σ^70 fragment (32) indicated as a black dashed line. In each panel, insertion starting and ending points are indicated by black spheres, the EM map is contoured at 2.6σ, and other ribbon colors are as in Fig. 2. Stereo pairs for B–E are shown in Figs. S6 and S7.

Figures were selected by an automated process.