PDBsum entry 1qyp

Transcription

PDB id: 1qyp

Contents

Protein chain

57 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1qyp

Name:

Transcription

Title:

Thermococcus celer rpb9, nmr, 25 structures

Structure:

RNA polymerase ii. Chain: a. Fragment: subunit rpb9, c-terminal domain, residues 58 -110. Engineered: yes

Source:

Thermococcus celer. Organism_taxid: 2264. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

25 models

Authors:

B.Wang,D.N.M.Jones,B.P.Kaine,M.A.Weiss

Key ref:

B.Wang et al. (1998). High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure, 6, 555-569. PubMed id: 9634694 DOI: 10.1016/S0969-2126(98)00058-6

Date:

19-Aug-97 Release date: 24-Dec-97

Protein chain

Q56254  (TFS_THECE) -  Transcription factor S from Thermococcus celer

Seq: 110 a.a.

Struc: 57 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(98)00058-6

Structure 6:555-569 (1998)

PubMed id: 9634694

High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases.

B.Wang, D.N.Jones, B.P.Kaine, M.A.Weiss.

ABSTRACT

BACKGROUND: Transcriptional initiation and elongation provide control points in gene expression. Eukaryotic RNA polymerase II subunit 9 (RPB9) regulates start-site selection and elongational arrest. RPB9 contains Cys4 Zn(2+)-binding motifs which are conserved in archaea and homologous to those of the general transcription factors TFIIB and TFIIS. RESULTS: The structure of an RPB9 domain from the hyperthermophilic archaeon Thermococcus celer was determined at high resolution by NMR spectroscopy. The structure consists of an apical tetrahedral Zn(2+)-binding site, central beta sheet and disordered loop. Although the structure lacks a globular hydrophobic core, the two surfaces of the beta sheet each contain well ordered aromatic rings engaged in serial edge-to-face interactions. Basic sidechains are clustered near the Zn(2+)-binding site. The disordered loop contains sidechains conserved in TFIIS, including acidic residues essential for the stimulation of transcriptional elongation. CONCLUSIONS: The planar architecture of the RPB9 zinc ribbon-distinct from that of a conventional globular domain-can accommodate significant differences in the alignment of polar, non-polar and charged sidechains. Such divergence is associated with local and non-local changes in structure. The RPB9 structure is distinguished by a fourth beta strand (extending the central beta sheet) in a well ordered N-terminal segment and also differs from TFIIS (but not TFIIB) in the orientation of its apical Zn(2+)-binding site. Cys4 Zn(2+)-binding sites with distinct patterns of polar, non-polar and charged residues are conserved among unrelated RNAP subunits and predicted to form variant zinc ribbons.

Selected figure(s)

Figure 5.
Figure 5. Structures of Zn2+-binding `knuckles'. (a) Stereo view of the RPB9 Zn2+-binding region (knuckles). Structures of the RPB9 ensemble were superimposed with respect to the mainchain atoms of residues 13-31 and 41-55. Sulfur atoms are shown as yellow balls, and Zn2+ as a white sphere. Predicted amide-sulfur hydrogen bonds are shown in yellow dashed lines: K20 NH-C18 Sg, C21 NH-C18 Sg, K48 NH-C46 Sg, and C49 NH-C46 Sg; N23 NH-C21 Sg is not shown. The protein is otherwise depicted in red. (b) Superposition of the Zn2+-binding region of RPB9 (red) and TFIIS (green) aligned with respect to the mainchain atoms of residues 13-31 and 41-55.

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 555-569) copyright 1998.

Figure was selected by an automated process.