PDBsum entry 3clj

RNA binding protein

PDB id: 3clj

Contents

Protein chain

146 a.a. *

Ligands

SO4

GOL ×4

Waters ×56

* Residue conservation analysis

PDB id:

3clj

Name:

RNA binding protein

Title:

Structure of the RNA polymerase ii ctd-interacting domain of nrd1

Structure:

Protein nrd1. Chain: a. Fragment: ctd-interacting domain, unp residues 6-151. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Gene: nrd1. Expressed in: escherichia coli.

Resolution:

2.10Å R-factor: 0.193 R-free: 0.220

Authors:

L.Vasiljeva,M.Kim,H.Mutschler,S.Buratowski,A.Meinhart

Key ref:

L.Vasiljeva et al. (2008). The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Biol, 15, 795-804. PubMed id: 18660819 DOI: 10.1038/nsmb.1468

Date:

19-Mar-08 Release date: 29-Jul-08

Protein chain

P53617  (NRD1_YEAST) -  Protein NRD1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 575 a.a.

Struc: 146 a.a.*

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

DOI no: 10.1038/nsmb.1468

Nat Struct Biol 15:795-804 (2008)

PubMed id: 18660819

The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain.

L.Vasiljeva, M.Kim, H.Mutschler, S.Buratowski, A.Meinhart.

ABSTRACT

RNA polymerase II (Pol II) in Saccharomyces cerevisiae can terminate transcription via several pathways. To study how a mechanism is chosen, we analyzed recruitment of Nrd1, which cooperates with Nab3 and Sen1 to terminate small nucleolar RNAs and other short RNAs. Budding yeast contains three C-terminal domain (CTD) interaction domain (CID) proteins, which bind the CTD of the Pol II largest subunit. Rtt103 and Pcf11 act in mRNA termination, and both preferentially interact with CTD phosphorylated at Ser2. The crystal structure of the Nrd1 CID shows a fold similar to that of Pcf11, but Nrd1 preferentially binds to CTD phosphorylated at Ser5, the form found proximal to promoters. This indicates why Nrd1 cross-links near 5' ends of genes and why the Nrd1-Nab3-Sen1 termination pathway acts specifically at short Pol II-transcribed genes. Nrd1 recruitment to genes involves a combination of interactions with CTD and Nab3.

Selected figure(s)

Figure 3.
Left, the CTD-Ser2P peptide is modeled bound to Nrd1 by simple manual superposition of the Nrd1 CID onto the Pcf11 CID. Right, the longer CTD model was created by superimposing the extended CTD-Ser5P bound to mRNA capping enzyme (PDB 1P16) onto the extended region of the CTD-Ser2P bound to Pcf11. The overlapping stretch of the two CTDs consists of Ser7-Tyr1-Ser2. Notably, the position of the phosphate moiety from Ser5P coincides with the bound sulfate ion observed in the Nrd1 crystal structure. Blue arrows point out phosphorylated CTD residues; black arrows show residues mutated and tested for effects on CTD binding in Table 1.

Figure 4.
(a) Schematic diagram of Nrd1. RE/RS, arginine-, serine- and glutamate-rich region; P/Q, proline- and glutamine-rich region. (b) Phenotypic analysis of nrd1 6–214 and nrd1 151–214 deletions. The NRD1 plasmid shuffling strain EJS101-9d was transformed with pJC580, pRS415-Nrd1 6–214 or pRS415-Nrd1 151–214, and the wild-type NRD1/URA3 plasmid (pRS316-NRD1) was shuffled out on 5-fluoroorotic acid (5-FOA) medium at the indicated temperatures. (c) Phenotypic analysis of nrd1 6–150 and nrd1 151–214 alleles integrated into the genome. (d) Nrd1 residues 151–214 are responsible for interaction with Nab3. Expression of the wild-type (WT) and mutant TAP-tagged proteins Nrd1, Nrd1 6–214 and Nrd1 151–214 in extracts was monitored by immunoblotting for the Protein A module of the TAP tag (below, -TAP). Nrd1 protein complexes were purified using IgG resin, and association with Nab3 was analyzed with anti-Nab3 antibody (above). Note that the Protein A module on Nrd1 reacts with the secondary antibody. (e) The Nab3 and CTD binding regions of Nrd1 contribute to its interaction with Pol II in vivo.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 795-804) copyright 2008.

Figures were selected by an automated process.