PDBsum entry 5m3m

Transcription

PDB id: 5m3m

Contents

Protein chains

1462 a.a.

1166 a.a.

305 a.a.

212 a.a.

98 a.a.

131 a.a.

116 a.a.

69 a.a.

101 a.a.

44 a.a.

97 a.a.

131 a.a.

58 a.a.

192 a.a.

Ligands

SO4

Metals

_ZN ×7

PDB id:

5m3m

Name:

Transcription

Title:

Free monomeric RNA polymerase i at 4.0a resolution

Structure:

DNA-directed RNA polymerase i subunit rpa190. Chain: a. Synonym: DNA-directed RNA polymerase i 190 kda polypeptide,a190,DNA- directed RNA polymerase i largest subunit. DNA-directed RNA polymerase i subunit rpa135. Chain: b. Synonym: DNA-directed RNA polymerase i 135 kda polypeptide,a135,DNA- directed RNA polymerase i polypeptide 2,RNA polymerase i subunit 2. DNA-directed RNA polymerases i and iii subunit rpac1.

Source:

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

Authors:

S.Neyer,M.Kunz,C.Geiss,M.Hantsche,V.-V.Hodirnau,A.Seybert,C.Engel, M.P.Scheffer,P.Cramer,A.S.Frangakis

Key ref:

S.Neyer et al. (2016). Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature, 540, 607-610. PubMed id: 27842382 DOI: 10.1038/nature20561

Date:

15-Oct-16 Release date: 23-Nov-16

Protein chain

P10964  (RPA1_YEAST) -  DNA-directed RNA polymerase I subunit RPA190 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1664 a.a.

Struc: 1462 a.a.

Protein chain

P22138  (RPA2_YEAST) -  DNA-directed RNA polymerase I subunit RPA135 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1203 a.a.

Struc: 1166 a.a.

Protein chain

P07703  (RPAC1_YEAST) -  DNA-directed RNA polymerases I and III subunit RPAC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 335 a.a.

Struc: 305 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: 212 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: 98 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: 131 a.a.

Protein chain

P32529  (RPA12_YEAST) -  DNA-directed RNA polymerase I subunit RPA12 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 125 a.a.

Struc: 116 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: 69 a.a.

Protein chain

P28000  (RPAC2_YEAST) -  DNA-directed RNA polymerases I and III subunit RPAC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 142 a.a.

Struc: 101 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.

Protein chain

Q01080  (RPA49_YEAST) -  DNA-directed RNA polymerase I subunit RPA49 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 415 a.a.

Struc: 97 a.a.

Protein chain

P47006  (RPA34_YEAST) -  DNA-directed RNA polymerase I subunit RPA34 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 233 a.a.

Struc: 131 a.a.

Protein chain

P50106  (RPA14_YEAST) -  DNA-directed RNA polymerase I subunit RPA14 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 137 a.a.

Struc: 58 a.a.

Protein chain

P46669  (RPA43_YEAST) -  DNA-directed RNA polymerase I subunit RPA43 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 326 a.a.

Struc: 192 a.a.

Enzyme reactions

• Enzyme class 1: 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 2: Chains C, E, F, H, I, J, K, L, M, N, D, G: E.C.?

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

Added reference

DOI no: 10.1038/nature20561

Nature 540:607-610 (2016)

PubMed id: 27842382

Structure of RNA polymerase I transcribing ribosomal DNA genes.

S.Neyer, M.Kunz, C.Geiss, M.Hantsche, V.V.Hodirnau, A.Seybert, C.Engel, M.P.Scheffer, P.Cramer, A.S.Frangakis.

ABSTRACT

RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively.