PDBsum entry 3d9n

Transcription

PDB id: 3d9n

Contents

Protein chains

138 a.a. *

Ligands

PRO-SEP-TYR-SEP-PRO-THR-SER-PRO ×2

SO4 ×10

Waters ×246

* Residue conservation analysis

PDB id:

3d9n

Name:

Transcription

Title:

Snapshots of the RNA processing factor scaf8 bound to different phosphorylated forms of the carboxy-terminal domain of RNA-polymerase ii

Structure:

RNA-binding protein 16. Chain: a, b. Fragment: ctd interacting domain of scaf8, unp residues 1-136. Synonym: RNA-binding motif protein 16. Engineered: yes. Ctd-peptide. Chain: y, z. Engineered: yes

Source:

Homo sapiens. Man. Organism_taxid: 9606. Gene: rbm16, kiaa1116. Expressed in: escherichia coli. Synthetic: yes. Other_details: peptide derived from the conserved repeat sequence in RNA polymerase ii ctd

Resolution:

1.60Å R-factor: 0.173 R-free: 0.201

Authors:

R.Becker,B.Loll,A.Meinhart

Key ref:

R.Becker et al. (2008). Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II. J Biol Chem, 283, 22659-22669. PubMed id: 18550522 DOI: 10.1074/jbc.M803540200

Date:

27-May-08 Release date: 10-Jun-08

Protein chains

Q9UPN6  (SCAF8_HUMAN) -  SR-related and CTD-associated factor 8 from Homo sapiens

Seq: 1271 a.a.

Struc: 138 a.a.*

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

DOI no: 10.1074/jbc.M803540200

J Biol Chem 283:22659-22669 (2008)

PubMed id: 18550522

Snapshots of the RNA Processing Factor SCAF8 Bound to Different Phosphorylated Forms of the Carboxyl-terminal Domain of RNA Polymerase II.

R.Becker, B.Loll, A.Meinhart.

ABSTRACT

Concomitant with RNA polymerase II (Pol II) transcription, RNA maturation factors are recruited to the carboxyl-terminal domain (CTD) of Pol II, whose phosphorylation state changes during a transcription cycle. CTD phosphorylation triggers recruitment of functionally different factors involved in RNA processing and transcription termination; most of these factors harbor a conserved CTD interacting domain (CID). Orchestration of factor recruitment is believed to be conducted by CID recognition of distinct phosphorylated forms of the CTD. We show that the human RNA processing factor SCAF8 interacts weakly with the unphosphorylated CTD of Pol II. Upon phosphorylation, affinity for the CTD is increased; however, SCAF8 is promiscuous to the phosphorylation pattern on the CTD. Employing a combined structural and biophysical approach, we were able to distinguish motifs within CIDs that are involved in a generic CTD sequence recognition from items that confer phospho-specificity.

Selected figure(s)

Figure 1.
FIGURE 1. SCAF8-CID binding to different phosphorylated forms of the CTD measured by fluorescence anisotropy competition titration experiments. Data points of the reference measurement of SCAF8-CID titrated to 2 µM FAM-Ser(P)-2-CTD peptide are presented as filled circles ( ). Data points for competition experiments where 100 µM concentrations of different non-fluorescently labeled CTD peptides competed against 2 µM FAM-Ser(P)-2-CTD peptide are given as open symbols. Fluorescence anisotropy data using Ser(P)-2/Ser(P)-5-CTD peptide are presented as open diamonds ( ) (K[d] = 19 (+/- 2/2) µM), Ser(P)-2-CTD peptide as open circles ( ) (K[d] = 68 (+/- 8/6) µM), Ser(P)-2/Ser(P)-7-CTD as open squares ( ) (K[d] = 90 (+/- 4/3) µM), and Ser(P)-5-CTD as inverted open triangles ( ) (K[d] = 330 (+/- 50/30) µM). The lines represent the best fit to data of individual measurements.

Figure 3.
FIGURE 3. A gallery of SCAF8-CID binding to different phospho forms of the CTD. SCAF8-CID is shown as a ribbon representation; the CTD is shown as a stick model. Hydrogen bonds between SCAF8-CID and the CTD are illustrated as black dashed lines, and intramolecular hydrogen bonds within the β-turn of the CTD are in orange. 2F[o] - F[c] electron density contoured at 0.9 for the bound CTD-peptides is illustrated beneath each model. Shown is SCAF8-CID binding Ser(P)-2/Ser(P)-5-CTD (PDB code 3D9K) (A), Ser(P)-2-CTD (PDB code 3D9L) (B), Ser(P)-5-CTD (PDB code 3D9M) (C), unphosphorylated CTD (PDB code 3D9O) (D), and Ser(P)-2/Ser(P)-7-CTD (PDB code 3D9N) (E) and Pcf11-CID (PDB code 1SZA) binding Ser(P)-2-CTD (F).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 22659-22669) copyright 2008.

Figures were selected by an automated process.