PDBsum entry 4c2m

Transcription

PDB id: 4c2m

Contents

Protein chains

44 a.a.

103 a.a.

145 a.a.

54 a.a.

1521 a.a.

1182 a.a.

305 a.a.

58 a.a.

212 a.a.

100 a.a.

193 a.a.

131 a.a.

124 a.a.

69 a.a.

101 a.a.

108 a.a.

145 a.a.

59 a.a.

Ligands

SO4 ×2

Metals

_ZN ×14

Waters ×262

PDB id:

4c2m

Name:

Transcription

Title:

Structure of RNA polymerase i at 2.8 a resolution

Structure:

DNA-directed RNA polymerases i, ii, and iii subunit rpabc 4. Chain: 1, l. Synonym: RNA polymerases i\,ii\,and iii subunit abc4, abc10-alpha, rpb12. DNA-directed RNA polymerase i subunit rpa49. Chain: 2, m. Synonym: a49, DNA-directed RNA polymerase i 49 kda polypeptide. DNA-directed RNA polymerase i subunit rpa34.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: cb010. Strain: cb010

Resolution:

2.80Å R-factor: 0.170 R-free: 0.210

Authors:

C.Engel,S.Sainsbury,A.C.Cheung,D.Kostrewa,P.Cramer

Key ref:

C.Engel et al. (2013). RNA polymerase I structure and transcription regulation. Nature, 502, 650-655. PubMed id: 24153182 DOI: 10.1038/nature12712

Date:

19-Aug-13 Release date: 23-Oct-13

Protein chains

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: 103 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: 145 a.a.

Protein chains

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

Seq: 326 a.a.

Struc: 54 a.a.

Protein chains

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

Seq: 1664 a.a.

Struc: 1521 a.a.

Protein chains

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

Seq: 1203 a.a.

Struc: 1182 a.a.

Protein chains

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

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 chains

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 chains

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: 100 a.a.

Protein chains

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

Seq: 326 a.a.

Struc: 193 a.a.

Protein chains

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 chains

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

Seq: 125 a.a.

Struc: 124 a.a.

Protein chains

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 chains

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

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

Seq: 415 a.a.

Struc: 108 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: 145 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: 59 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, P, Q: 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/nature12712

Nature 502:650-655 (2013)

PubMed id: 24153182

RNA polymerase I structure and transcription regulation.

C.Engel, S.Sainsbury, A.C.Cheung, D.Kostrewa, P.Cramer.

ABSTRACT

Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I from the yeast Saccharomyces cerevisiae at 2.8 Å resolution reveals all 14 subunits of the 590-kilodalton enzyme, and shows differences to Pol II. An 'expander' element occupies the DNA template site and stabilizes an expanded active centre cleft with an unwound bridge helix. A 'connector' element invades the cleft of an adjacent polymerase and stabilizes an inactive polymerase dimer. The connector and expander must detach during Pol I activation to enable transcription initiation and cleft contraction by convergent movement of the polymerase 'core' and 'shelf' modules. Conversion between an inactive expanded and an active contracted polymerase state may generally underlie transcription. Regulatory factors can modulate the core-shelf interface that includes a 'composite' active site for RNA chain initiation, elongation, proofreading and termination.