PDBsum entry 4y7n

Transcription/DNA/RNA

PDB id: 4y7n

Contents

Protein chains

1393 a.a.

1103 a.a.

266 a.a.

214 a.a.

84 a.a.

133 a.a.

119 a.a.

65 a.a.

114 a.a.

44 a.a.

DNA/RNA

Ligands

G2P

Metals

_MG ×2

_ZN ×8

PDB id:

4y7n

Name:

Transcription/DNA/RNA

Title:

The structure insight into 5-carboxycytosine recognition by RNA polymerase ii during transcription elongation.

Structure:

DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit b1,DNA-directed RNA polymerase iii largest subunit,RNA polymerase ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2,DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2,b150,DNA-directed RNA polymerase ii 140 kda polypeptide,RNA polymerase ii subunit 2,b150,DNA-directed

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Resolution:

3.30Å R-factor: 0.209 R-free: 0.250

Authors:

L.Wang,J.Chong,D.Wang

Key ref:

L.Wang et al. (2015). Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex. Nature, 523, 621-625. PubMed id: 26123024 DOI: 10.1038/nature14482

Date:

15-Feb-15 Release date: 15-Jul-15

Protein chain

P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1733 a.a.

Struc: 1393 a.a.

Protein chain

P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1224 a.a.

Struc: 1103 a.a.

Protein chain

P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 318 a.a.

Struc: 266 a.a.

Protein chain

P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 214 a.a.

Protein chain

P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 155 a.a.

Struc: 84 a.a.

Protein chain

P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 146 a.a.

Struc: 133 a.a.

Protein chain

P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 122 a.a.

Struc: 119 a.a.

Protein chain

P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 70 a.a.

Struc: 65 a.a.

Protein chain

P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 120 a.a.

Struc: 114 a.a.

Protein chain

P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 70 a.a.

Struc: 44 a.a.

DNA/RNA chains

C-T-A-C-C-G-A-T-A-A-G-C-A-G-A-C-G-A-1CC-C-C-T-C-T-C-C-A-T-G 29 bases

C-T-G-C-T-T-A-T-C-G-G-T-A-G 14 bases

A-U-G-G-A-G-A-G-G 9 bases

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

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

Added reference

DOI no: 10.1038/nature14482

Nature 523:621-625 (2015)

PubMed id: 26123024

Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.

L.Wang, Y.Zhou, L.Xu, R.Xiao, X.Lu, L.Chen, J.Chong, H.Li, C.He, X.D.Fu, D.Wang.

ABSTRACT

DNA methylation at selective cytosine residues (5-methylcytosine (5mC)) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development. TET enzymes successively convert 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), with 5fC and 5caC subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair. Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters and gene bodies, with distinct effects on gene expression, but the mechanisms have remained elusive. Here we determined the X-ray crystal structure of yeast elongating RNA polymerase II (Pol II) in complex with a DNA template containing oxidized 5mCs, revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming nucleoside 5'-triphosphate (NTP), thus compromising nucleotide addition. To test the implication of this structural insight in vivo, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxidized 5mCs on gene expression and suggest a novel role for Pol II as a specific and direct epigenetic sensor during transcription elongation.