PDBsum entry 4ayb

Transferase

PDB id: 4ayb

Contents

Protein chains

872 a.a.

1103 a.a.

376 a.a.

262 a.a.

171 a.a.

105 a.a.

113 a.a.

76 a.a.

84 a.a.

91 a.a.

65 a.a.

44 a.a.

50 a.a.

Ligands

SF4

Metals

_MG

_ZN ×10

PDB id:

4ayb

Name:

Transferase

Title:

Rnap at 3.2ang

Structure:

DNA-directed RNA polymerase. Chain: a. Other_details: rpo1n subunit. DNA-directed RNA polymerase. Chain: b. Other_details: rpo2. DNA-directed RNA polymerase. Chain: c. Other_details: rpo1c.

Source:

Sulfolobus shibatae. Archaea. Organism_taxid: 2286. Organism_taxid: 2286

Resolution:

3.20Å R-factor: 0.245 R-free: 0.301

Authors:

M.N.Wojtas,M.Mogni,O.Millet,S.D.Bell,N.G.A.Abrescia

Key ref:

M.N.Wojtas et al. (2012). Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA. Nucleic Acids Res, 40, 9941-9952. PubMed id: 22848102

Date:

19-Jun-12 Release date: 08-Aug-12

Protein chain

B8YB53  (B8YB53_SULSH) -  DNA-directed RNA polymerase subunit Rpo1N from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 880 a.a.

Struc: 872 a.a.

Protein chain

B8YB55  (B8YB55_SULSH) -  DNA-directed RNA polymerase subunit Rpo2 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 1128 a.a.

Struc: 1103 a.a.

Protein chain

B8YB54  (B8YB54_SULSH) -  DNA-directed RNA polymerase subunit Rpo1C from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 392 a.a.

Struc: 376 a.a.

Protein chain

B8YB56  (B8YB56_SULSH) -  DNA-directed RNA polymerase subunit Rpo3 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 265 a.a.

Struc: 262 a.a.

Protein chain

B8YB57  (B8YB57_SULSH) -  DNA-directed RNA polymerase subunit Rpo7 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 180 a.a.

Struc: 171 a.a.

Protein chain

B8YB58  (B8YB58_SULSH) -  DNA-directed RNA polymerase subunit Rpo4 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 113 a.a.

Struc: 105 a.a.

Protein chain

B8YB59  (B8YB59_SULSH) -  DNA-directed RNA polymerase subunit Rpo8 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 131 a.a.

Struc: 113 a.a.

Protein chain

B8YB60  (B8YB60_SULSH) -  DNA-directed RNA polymerase subunit Rpo5 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 84 a.a.

Struc: 76 a.a.

Protein chain

B8YB61  (B8YB61_SULSH) -  DNA-directed RNA polymerase subunit Rpo6 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 95 a.a.

Struc: 84 a.a.

Protein chain

B8YB62  (B8YB62_SULSH) -  DNA-directed RNA polymerase subunit Rpo11 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 92 a.a.

Struc: 91 a.a.

Protein chain

B8YB63  (B8YB63_SULSH) -  DNA-directed RNA polymerase subunit Rpo10 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 66 a.a.

Struc: 65 a.a.

Protein chain

B8YB64  (B8YB64_SULSH) -  DNA-directed RNA polymerase subunit Rpo12 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 48 a.a.

Struc: 44 a.a.

Protein chain

B8YB65  (B8YB65_SULSH) -  DNA-directed RNA polymerase subunit Rpo13 from Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)

Seq: 104 a.a.

Struc: 50 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, K, L, N, 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

Nucleic Acids Res 40:9941-9952 (2012)

PubMed id: 22848102

Structural and functional analyses of the interaction of archaeal RNA polymerase with DNA.

M.N.Wojtas, M.Mogni, O.Millet, S.D.Bell, N.G.Abrescia.

ABSTRACT

Multi-subunit RNA polymerases (RNAPs) in all three domains of life share a common ancestry. The composition of the archaeal RNAP (aRNAP) is not identical between phyla and species, with subunits Rpo8 and Rpo13 found in restricted subsets of archaea. While Rpo8 has an ortholog, Rpb8, in the nuclear eukaryal RNAPs, Rpo13 lacks clear eukaryal orthologs. Here, we report crystal structures of the DNA-bound and free form of the aRNAP from Sulfolobus shibatae. Together with biochemical and biophysical analyses, these data show that Rpo13 C-terminus binds non-specifically to double-stranded DNA. These interactions map on our RNAP-DNA binary complex on the downstream DNA at the far end of the DNA entry channel. Our findings thus support Rpo13 as a RNAP-DNA stabilization factor, a role reminiscent of eukaryotic general transcriptional factors. The data further yield insight into the mechanisms and evolution of RNAP-DNA interaction.