PDBsum entry 4c3i

Transferase

PDB id: 4c3i

Contents

Protein chains

1484 a.a.

1176 a.a.

304 a.a.

59 a.a.

215 a.a.

100 a.a.

259 a.a.

134 a.a.

124 a.a.

69 a.a.

103 a.a.

45 a.a.

105 a.a.

139 a.a.

Ligands

SO4 ×3

MPD

Metals

_ZN ×7

_MG

PDB id:

4c3i

Name:

Transferase

Title:

Structure of 14-subunit RNA polymerase i at 3.0 a resolution, crystal form c2-100

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 a190. 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

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: sc1613. Other_details: strain sc1613, alias ypr110c, provided by cellzome ag in heidelberg, germany, modified to express endogenous ac40 fused with a c-terminal tap-tag.. With a c-terminal tap-tag.

Resolution:

3.00Å R-factor: 0.200 R-free: 0.231

Authors:

C.Fernandez-Tornero,M.Moreno-Morcillo,U.J.Rashid,N.M.I.Taylor, F.M.Ruiz,T.Gruene,P.Legrand,U.Steuerwald,C.W.Muller

Key ref:

C.Fernández-Tornero et al. (2013). Crystal structure of the 14-subunit RNA polymerase I. Nature, 502, 644-649. PubMed id: 24153184 DOI: 10.1038/nature12636

Date:

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

Protein chain

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

Seq: 1664 a.a.

Struc: 1484 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: 1176 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: 304 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.*

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: 100 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: 259 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: 134 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: 124 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: 103 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: 45 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: 105 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: 139 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: 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 3: Chains C, D, E, F, G, H, I, J, K, L, M, N: 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/nature12636

Nature 502:644-649 (2013)

PubMed id: 24153184

Crystal structure of the 14-subunit RNA polymerase I.

C.Fernández-Tornero, M.Moreno-Morcillo, U.J.Rashid, N.M.Taylor, F.M.Ruiz, T.Gruene, P.Legrand, U.Steuerwald, C.W.Müller.

ABSTRACT

Protein biosynthesis depends on the availability of ribosomes, which in turn relies on ribosomal RNA production. In eukaryotes, this process is carried out by RNA polymerase I (Pol I), a 14-subunit enzyme, the activity of which is a major determinant of cell growth. Here we present the crystal structure of Pol I from Saccharomyces cerevisiae at 3.0 Å resolution. The Pol I structure shows a compact core with a wide DNA-binding cleft and a tightly anchored stalk. An extended loop mimics the DNA backbone in the cleft and may be involved in regulating Pol I transcription. Subunit A12.2 extends from the A190 jaw to the active site and inserts a transcription elongation factor TFIIS-like zinc ribbon into the nucleotide triphosphate entry pore, providing insight into the role of A12.2 in RNA cleavage and Pol I insensitivity to α-amanitin. The A49-A34.5 heterodimer embraces subunit A135 through extended arms, thereby contacting and potentially regulating subunit A12.2.