PDBsum entry: 2ja8

Transferase

PDB-id: 2ja8

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Description

Header details

Header records

References

PROCHECK

Protein chains

1421 a.a. *

1115 a.a. *

267 a.a. *

177 a.a. *

214 a.a. *

87 a.a. *

171 a.a. *

135 a.a. *

116 a.a. *

65 a.a. *

114 a.a. *

46 a.a. *

DNA/RNA

Metal ions

_ZN ×8

_MG

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2ja8

Name:

Transferase

Title:

Cpd lesion containing RNA polymerase ii elongation complex d

Structure:

DNA-directed RNA polymerase ii largest subunit. Chain: a. Synonym: RNA polymerase ii subunit 1, b220. DNA-directed RNA polymerase ii 140 kda polypeptide. Chain: b. Synonym: b150, RNA polymerase ii subunit 2. DNA-directed RNA polymerase ii 45kda polypeptide. Chain: c.

Source:

Saccharomyces cerevisiae. Bakers' yeast. Organism_taxid: 4932. Synthetic: yes. Other_details: synthetic oligonucleotide. Other_details: synthetic oligonucleotide

UniProt:

Chain A: P04050 (RPB1_YEAST)

Seq:
Struc:
	Seq:
	Struc:
Seq:
Struc:
	Seq:
	Struc:
Seq:
Struc:
	Seq:
	Struc:
Seq:		1733 a.a.
Struc:		1421 a.a.

Chain B: P08518 (RPB2_YEAST)

Seq:
Struc:
	Seq:
	Struc:
Seq:
Struc:
	Seq:
	Struc:
Seq:		1224 a.a.
Struc:		1115 a.a.

Chain C: P16370 (RPB3_YEAST)

Seq:
Struc:
	Seq:	318 a.a.
	Struc:	267 a.a.

Chain D: P20433 (RPB4_YEAST)

Seq:	221 a.a.
Struc:	177 a.a.

Chain E: P20434 (RPAB1_YEAST)

Seq:	215 a.a.
Struc:	214 a.a.

Chain F: P20435 (RPAB2_YEAST)

Seq:	155 a.a.
Struc:	87 a.a.

Chain G: P34087 (RPB7_YEAST)

Seq:	171 a.a.
Struc:	171 a.a.

Chain H: P20436 (RPAB3_YEAST)

Seq:	146 a.a.
Struc:	135 a.a.

Chain I: P27999 (RPB9_YEAST)

Seq:	122 a.a.
Struc:	116 a.a.

Chain J: P22139 (RPAB5_YEAST)

Seq:	70 a.a.
Struc:	65 a.a.

Chain K: P38902 (RPB11_YEAST)

Seq:	120 a.a.
Struc:	114 a.a.

Chain L: P40422 (RPAB4_YEAST)

Seq:

70 a.a.

Struc:

46 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

Chains A, B: E.C.2.7.7.6   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1) (see diagram below)

Resolution:

3.80Å

R-factor:

0.268

R-free:

0.287

Authors:

F.Brueckner,U.Hennecke,T.Carell,P.Cramer

Key ref:

F.Brueckner et al. (2007). CPD Damage Recognition by Transcribing RNA Polymerase II.. Science, 315, 859-862. [PubMed id: 17290000] [DOI: 10.1126/science.1135400]

Date:

23-Nov-06

Release date:

20-Feb-07

Related entries:

1i3q RNA polymerase ii crystal form i at 3.1 a resolution
1i50 RNA polymerase ii crystal form ii at 2.8 a resolution
1i6h RNA polymerase ii elongation complex
1k83 crystal structure of yeast RNA polymerase ii complexed withthe inhibitor alpha amanitin
1nik wild type RNA polymerase ii
1nt9 complete 12-subunit RNA polymerase ii
1pqv RNA polymerase ii-tfiis complex
1r5u RNA polymerase ii tfiib complex
1r9s RNA polymerase ii strand separated elongation complex,matched nucleotide
1r9t RNA polymerase ii strand separated elongation complex,mismatched nucleotide
... plus others (see Header records)

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Procheck

Key reference

DOI no: 10.1126/science.1135400

Science 315:859-862 (2007)

PubMed id: 17290000

CPD Damage Recognition by Transcribing RNA Polymerase II.

F.Brueckner, U.Hennecke, T.Carell, P.Cramer.

ABSTRACT

Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5'-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.

Selected figure(s)

Figure 1.
Fig. 1. Pol II elongation complex structures with thymine-thymine CPD lesions in the template. (A) Nucleic acid scaffolds A to D. The color code is used throughout. Filled circles denote nucleotides with interpretable electron density that were included in the structures in (B). Open circles denote nucleotides having electron density that could not be interpreted or that was lacking. (B) Structure of nucleic acids in the Pol II elongation complexes A to D. The view is from the side (11). Figures prepared with PYMOL (DeLano Scientific). (C) Overview of complex C with a CPD lesion at the active site. The view is as in (B). Protein is in gray, the bridge helix in green. The CPD is shown as a stick model in orange. A large portion of the second largest Pol II subunit was omitted for clarity. (D) Superposition of nucleic acids in structures A to D. The protein molecules were superimposed and then omitted. The nucleic acids are depicted as ribbon models, the CPDs as stick models. Upper and lower views are related by a 90° rotation around a horizontal axis.

Figure 3.
Fig. 3. Mechanism of CPD recognition by transcribing Pol II. Schematic representation of RNA extension in complex A. The initial RNA (top) corresponds to the nonextended RNA of scaffold A. The translocation barrier and the translocation block are indicated with a dashed and a solid horizontal line, respectively. The artificial situation leading to lesion bypass (Fig. 2E) is depicted at the bottom.

The above figures are reprinted by permission from the AAAs: Science (2007, 315, 859-862) copyright 2007.

Figures were selected by the author.