PDBsum entry: 1i6h

Transcription/DNA-RNA hybrid

PDB id: 1i6h

Contents

Protein chains

1381 a.a. *

1097 a.a. *

266 a.a. *

214 a.a. *

84 a.a. *

133 a.a. *

119 a.a. *

65 a.a. *

114 a.a. *

46 a.a. *

DNA/RNA

Metals

_ZN ×8

_MG

* Residue conservation analysis

PDB id:

1i6h

Name:

Transcription/DNA-RNA hybrid

Title:

RNA polymerase ii elongation complex

Structure:

5'-d(p Ap Ap Ap Tp Gp Cp Cp Tp Gp Gp Tp Cp T)-3'. Chain: d. Engineered: yes. Other_details: template. 5'-r(p Gp Ap Cp Cp Ap Gp Gp Cp A)-3'. Chain: r. Engineered: yes. Other_details: transcript. DNA-directed RNA polymerase ii largest subunit.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Synthetic: yes. Other_details: the RNA was synthesized by the polymerase before the crystal was formed.. Strain: delta-rpb4. Strain: delta-rpb4

Biol. unit:

24mer (from PQS)

Resolution:

3.30Å R-factor: 0.250 R-free: 0.298

Authors:

A.L.Gnatt,P.Cramer,R.D.Kornberg

Key ref:

A.L.Gnatt et al. (2001). Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science, 292, 1876-1882. PubMed id: 11313499 DOI: 10.1126/science.1059495

Date:

02-Mar-01 Release date: 23-Apr-01

Protein chain

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

Seq: 1733 a.a.

Struc: 1381 a.a.

Protein chain

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

Seq: 1224 a.a.

Struc: 1097 a.a.

Protein chain

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

Seq: 318 a.a.

Struc: 266 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

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.

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 (9 terms)
• Biological process: response to DNA damage stimulus (12 terms)
• Biochemical function: transcription regulator activity (11 terms)

reference

DOI no: 10.1126/science.1059495

Science 292:1876-1882 (2001)

PubMed id: 11313499

Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.

A.L.Gnatt, P.Cramer, J.Fu, D.A.Bushnell, R.D.Kornberg.

ABSTRACT

The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.

Selected figure(s)

Figure 5.
Fig. 5. DNA-RNA hybrid conformation. The view is similar to that in Fig. 2C. The conformation of the DNA-RNA hybrid is intermediary between canonical A- and B-DNA. DNA, blue; RNA, red.

Figure 6.
Fig. 6. Proposed transcription cycle and translocation mechanism. (A) Schematic representation of the nucleotide addition cycle. The nucleotide triphosphate (NTP) fills the open substrate site (top) and forms a phosphodiester bond at the active site ("Synthesis"). This results in the state of the transcribing complex seen in the crystal structure (middle). We speculate that "Translocation" of the nucleic acids with respect to the active site (marked by a pink dot for metal A) involves a change of the bridge helix from a straight (silver circle) to a bent conformation (violet circle, bottom). Relaxation of the bridge helix back to a straight conformation without movement of the nucleic acids would result in an open substrate site one nucleotide downstream and would complete the cycle. (B) Different conformations of the bridge helix in pol II and bacterial RNA polymerase structures. The view is the same as in Fig. 2C. The bacterial RNA polymerase structure (2) was superimposed on the pol II transcribing complex by fitting residues around the active site. The resulting fit of the bridge helices of pol II (silver) and the bacterial polymerase (violet) is shown. The bend in the bridge helix in the bacterial polymerase structure causes a clash of amino acid side chains (extending from the backbone shown here) with the hybrid base pair at position +1.

The above figures are reprinted by permission from the AAAs: Science (2001, 292, 1876-1882) copyright 2001.

Figures were selected by the author.