PDBsum entry 5flm

Transcription

PDB id: 5flm

Contents

Protein chains

1427 a.a.

1134 a.a.

257 a.a.

128 a.a.

209 a.a.

82 a.a.

171 a.a.

148 a.a.

114 a.a.

67 a.a.

115 a.a.

44 a.a.

DNA/RNA

Metals

_MG

_ZN ×8

PDB id:

5flm

Name:

Transcription

Title:

Structure of transcribing mammalian RNA polymerase ii

Structure:

DNA-directed RNA polymerase. Chain: a. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: DNA-directed RNA polymerase ii 140 kda polypeptide, DNA- directed RNA polymerase ii subunit b, RNA polymerase ii subunit 2, RNA polymerase ii subunit b2. DNA-directed RNA polymerase ii subunit rpb3. Chain: c.

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Tissue: thymus. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630

Authors:

C.Bernecky,F.Herzog,W.Baumeister,J.M.Plitzko,P.Cramer

Key ref:

C.Bernecky et al. (2016). Structure of transcribing mammalian RNA polymerase II. Nature, 529, 551-554. PubMed id: 26789250 DOI: 10.1038/nature16482

Date:

26-Oct-15 Release date: 20-Jan-16

Protein chain

G3MZY8  (G3MZY8_BOVIN) -  DNA-directed RNA polymerase II subunit RPB1 from Bos taurus

Seq: 1970 a.a.

Struc: 1427 a.a.

Protein chain

A5PJW8  (A5PJW8_BOVIN) -  DNA-directed RNA polymerase II subunit RPB2 from Bos taurus

Seq: 1174 a.a.

Struc: 1134 a.a.

Protein chain

Q3T0Q3  (RPB3_BOVIN) -  DNA-directed RNA polymerase II subunit RPB3 from Bos taurus

Seq: 275 a.a.

Struc: 257 a.a.

Protein chain

Q1JQ91  (Q1JQ91_BOVIN) -  DNA-directed RNA polymerase II subunit RPB4 from Bos taurus

Seq: 142 a.a.

Struc: 128 a.a.

Protein chain

Q2T9T3  (RPAB1_BOVIN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Bos taurus

Seq: 210 a.a.

Struc: 209 a.a.

Protein chain

Q32PE0  (RPAB2_BOVIN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Bos taurus

Seq: 127 a.a.

Struc: 82 a.a.

Protein chain

Q5E9B8  (RPB7_BOVIN) -  DNA-directed RNA polymerase II subunit RPB7 from Bos taurus

Seq: 172 a.a.

Struc: 171 a.a.

Protein chain

F2Z4H3  (F2Z4H3_BOVIN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Bos taurus

Seq: 150 a.a.

Struc: 148 a.a.

Protein chain

Q32P73  (RPB9_BOVIN) -  DNA-directed RNA polymerase II subunit RPB9 from Bos taurus

Seq: 125 a.a.

Struc: 114 a.a.

Protein chain

Q32P78  (RPAB5_BOVIN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Bos taurus

Seq: 67 a.a.

Struc: 67 a.a.

Protein chain

Q32P79  (RPB11_BOVIN) -  DNA-directed RNA polymerase II subunit RPB11 from Bos taurus

Seq: 117 a.a.

Struc: 115 a.a.

Protein chain

Q3ZBC0  (RPAB4_BOVIN) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4 from Bos taurus

Seq: 58 a.a.

Struc: 44 a.a.

DNA/RNA chains

G-G-C-A-G-T-A-C-T-A-G-T-A-A-A-G-T-A-C-T-T-G-A-G-C-T-T 27 bases

C-A-U-A-A-A-G-A-C-C-A-G-G-C 14 bases

A-A-G-C-T-C-A-A-G-T-A-C-T-T-A-A-G-C-C-T-G-G-T-C-A-T-T-A-C-T-A-G-T-A-C-T-G-C-C 39 bases

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B: E.C.3.1.13.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nature16482

Nature 529:551-554 (2016)

PubMed id: 26789250

Structure of transcribing mammalian RNA polymerase II.

C.Bernecky, F.Herzog, W.Baumeister, J.M.Plitzko, P.Cramer.

ABSTRACT

RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription.