PDBsum entry: 1pqv

Transferase/transcription

PDB id: 1pqv

Contents

Protein chains

1409 a.a.* *

1103 a.a.* *

266 a.a.* *

135 a.a.* *

214 a.a.* *

84 a.a.* *

169 a.a.* *

133 a.a.* *

119 a.a.* *

65 a.a.* *

114 a.a.* *

46 a.a.* *

174 a.a.* *

Metals

_ZN ×9

_MG

* Residue conservation analysis

* C-alpha coords only

PDB id:

1pqv

Name:

Transferase/transcription

Title:

RNA polymerase ii-tfiis complex

Structure:

DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: b220. DNA-directed RNA polymerase ii 140 kda polypeptide. Chain: b. Synonym: b150. RNA polymerase ii subunit 2. DNA-directed RNA polymerase ii 45 kda polypeptide.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932

Biol. unit:

30mer (from PQS)

Resolution:

3.80Å R-factor: not given

Authors:

H.Kettenberger,K.-J.Armache,P.Cramer

Key ref:

H.Kettenberger et al. (2003). Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell, 114, 347-357. PubMed id: 12914699 DOI: 10.1016/S0092-8674(03)00598-1

Date:

19-Jun-03 Release date: 19-Aug-03

Protein chain

P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1

Seq: 1733 a.a.

Struc: 1409 a.a.

Protein chain

P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2

Seq: 1224 a.a.

Struc: 1103 a.a.

Protein chain

P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3

Seq: 318 a.a.

Struc: 266 a.a.

Protein chain

P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4

Seq: 221 a.a.

Struc: 135 a.a.*

Protein chain

P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1

Seq: 215 a.a.

Struc: 214 a.a.

Protein chain

P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2

Seq: 155 a.a.

Struc: 84 a.a.

Protein chain

P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7

Seq: 171 a.a.

Struc: 169 a.a.

Protein chain

P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3

Seq: 146 a.a.

Struc: 133 a.a.

Protein chain

P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9

Seq: 122 a.a.

Struc: 119 a.a.

Protein chain

P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5

Seq: 70 a.a.

Struc: 65 a.a.

Protein chain

P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11

Seq: 120 a.a.

Struc: 114 a.a.

Protein chain

P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4

Seq: 70 a.a.

Struc: 46 a.a.

Protein chain

P07273  (TFS2_YEAST) -  Transcription elongation factor S-II

Seq: 309 a.a.

Struc: 174 a.a.

* PDB and UniProt seqs differ at 29 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: RNA polymerase complex (10 terms)
• Biological process: cellular metabolic process (23 terms)
• Biochemical function: catalytic activity (20 terms)

reference

DOI no: 10.1016/S0092-8674(03)00598-1

Cell 114:347-357 (2003)

PubMed id: 12914699

Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.

H.Kettenberger, K.J.Armache, P.Cramer.

ABSTRACT

The transcription elongation factor TFIIS induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II. We have diffused TFIIS into Pol II crystals and derived a model of the Pol II-TFIIS complex from X-ray diffraction data to 3.8 A resolution. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 A. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active center. Our results support the idea that Pol II contains a single tunable active site for RNA polymerization and cleavage, in contrast to DNA polymerases with two separate active sites for DNA polymerization and cleavage.

Selected figure(s)

Figure 4.
Figure 4. Model of a Pol II-TFIIS-Nucleic Acid Complex(A) Side view. The DNA template strand (blue) and the RNA transcript (red) were placed onto the model of Figure 2B according to their location in the elongation complex structure (Gnatt et al., 2001). The Rpb2 protrusion, fork, and external domains were omitted for clarity. The presumed location of backtracked RNA is indicated as a dashed red ribbon. The arrows indicate movement of Pol II relative to the nucleic acids.(B) Cut-away view of the model in (A) from the front. TFIIS and nucleic acids are shown as ribbon models on the molecular surface of Pol II, which is cut along the vertical slice plane indicated in (A). The presumed path of backtracked RNA through the restricted pore is drawn as a dashed red ribbon. The backtracked portion of RNA would be cut at the active site during TFIIS-induced RNA cleavage.(C) Proximity of the TFIIS acidic hairpin to the potential scissile RNA phosphodiester bond. The view is as in (A). RNA was placed according to the location in the Pol II elongation complex structure (Gnatt et al., 2001), and is shown as a stick model with phosphorous atoms highlighted as blue spheres. The black arrow indicates the direction of a possible S[N]2-type nucleophilic in-line attack of the scissile bond (blue).

Figure 5.
Figure 5. TFIIS-Induced Structural Changes in Pol II(A) Local remodeling of the Pol II active center. Structural elements of the active center in the Pol II-TFIIS complex are shown as ribbons in different colors. The corresponding elements in the free 12-subunit Pol II structure are shown superimposed in beige. In the Pol II-TFIIS complex, the trigger loop (blue) and fork loop 2 (pink) are folded, parts of the bridge helix (cyan) are shifted upward, and switches 1 and 2 (red and purple, respectively) moved outward. The DNA template strand (blue) and product RNA (red) have been placed according to the Pol II elongation complex structure (Gnatt et al., 2001). A pink sphere marks the location of metal ion A (Cramer et al. 2000 and Cramer et al. 2001).(B) Opening of the Pol II crevice and insertion of the TFIIS linker. Detailed view of the TFIIS linker (yellow) passing through the crevice (magenta). The location of the two crevice-forming elements in free Pol II is shown in beige. The view is from the bottom, as in Figure 2 and Figure 3.(C–E) Global repositioning of the Pol II mobile mass. In (C), regions of the model in Figure 2B that are repositioned upon TFIIS binding (mobile mass) are highlighted in magenta. In (D), changes in the mobile mass between free Pol II (beige) and the Pol II-TFIIS complex (magenta) are shown. The models were superimposed based on the unchanged regions in the Pol II core module (Cramer et al., 2001). Arrows indicate the direction and magnitude of movements at outer positions. The location of the incoming DNA duplex during transcription elongation is indicated as a dashed blue circle. In (E), Pol II regions contributing to the mobile mass are shown. Subunits are colored according to the color code used previously (Armache et al. 2003; Cramer et al. 2000 and Cramer et al. 2001).

The above figures are reprinted by permission from Cell Press: Cell (2003, 114, 347-357) copyright 2003.

Figures were selected by the author.