PDBsum entry 4by7

Transcription

PDB id: 4by7

Contents

Protein chains

1426 a.a.

1115 a.a.

266 a.a.

178 a.a.

215 a.a.

87 a.a.

171 a.a.

133 a.a.

119 a.a.

65 a.a.

115 a.a.

46 a.a.

119 a.a.

DNA/RNA

Ligands

EPE ×2

Metals

_ZN ×8

_MG

PDB id:

4by7

Name:

Transcription

Title:

Elongating RNA polymerase ii-bye1 tld complex

Structure:

DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit 1, RNA polymerase ii subunit b1, DNA-directed RNA polymerase iii largest subunit, RNA polymerase ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2, b150, DNA-directed RNA polymerase ii 140 kda polypeptide.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: ril.

Resolution:

3.15Å R-factor: 0.190 R-free: 0.212

Authors:

K.Kinkelin,G.G.Wozniak,S.B.Rothbart,M.Lidschreiber,B.D.Strahl, P.Cramer

Key ref:

K.Kinkelin et al. (2013). Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue. Proc Natl Acad Sci U S A, 110, 15277-15282. PubMed id: 24003114 DOI: 10.1073/pnas.1311010110

Date:

18-Jul-13 Release date: 11-Sep-13

Protein chain

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

Seq: 1733 a.a.

Struc: 1426 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: 1115 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

P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 221 a.a.

Struc: 178 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: 215 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: 87 a.a.

Protein chain

P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 171 a.a.

Struc: 171 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: 115 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: 46 a.a.

Protein chain

P36106  (BYE1_YEAST) -  Transcription factor BYE1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 594 a.a.

Struc: 119 a.a.

DNA/RNA chains

A-A-A-G-T-A-C-T-T-G-A-G-C 13 bases

U-C-G-A-C-C-A-G-G-A 10 bases

G-C-T-C-A-A-G-T-A-C-T-T-A-T-T-C-C-BRU-G-G-T-C-A-T-T 25 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: 10.1073/pnas.1311010110

Proc Natl Acad Sci U S A 110:15277-15282 (2013)

PubMed id: 24003114

Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue.

K.Kinkelin, G.G.Wozniak, S.B.Rothbart, M.Lidschreiber, B.D.Strahl, P.Cramer.

ABSTRACT

Bypass of Ess1 (Bye1) is a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. Here we show that Bye1 binds with its TFIIS-like domain (TLD) to RNA polymerase (Pol) II, and report crystal structures of the Bye1 TLD bound to Pol II and three different Pol II-nucleic acid complexes. Like TFIIS, Bye1 binds with its TLD to the Pol II jaw and funnel. In contrast to TFIIS, however, it neither alters the conformation nor the in vitro functions of Pol II. In vivo, Bye1 is recruited to chromatin via its TLD and occupies the 5'-region of active genes. A plant homeo domain (PHD) in Bye1 binds histone H3 tails with trimethylated lysine 4, and this interaction is enhanced by the presence of neighboring posttranslational modifications (PTMs) that mark active transcription and conversely is impaired by repressive PTMs. We identify putative human homologs of Bye1, the proteins PHD finger protein 3 and death-inducer obliterator, which are both implicated in cancer. These results establish Bye1 as the founding member of a unique family of chromatin transcription factors that link histones with active PTMs to transcribing Pol II.