PDBsum entry 5d4c

Transcription/DNA

PDB id: 5d4c

Contents

Protein chains

231 a.a.

1112 a.a.

1486 a.a.

94 a.a.

346 a.a.

DNA/RNA

Ligands

C5P ×2

CTP ×2

ATP ×2

Metals

_MG ×11

_ZN ×4

Waters ×58

PDB id:

5d4c

Name:

Transcription/DNA

Title:

Crystal structure of thermus thermophilus product complex for transcription initiation with atp and ctp

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b, k, l. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. DNA-directed RNA polymerase subunit beta. Chain: c, m. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta. DNA-directed RNA polymerase subunit beta'.

Source:

Thermus thermophilus. Organism_taxid: 274. Thermus thermophilus (strain hb8 / atcc 27634 / dsm 579). Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Gene: siga, ttha0532. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

3.28Å R-factor: 0.214 R-free: 0.257

Authors:

Y.Zhang,R.H.Ebright

Key ref:

J.G.Bird et al. (2016). The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature, 535, 444-447. PubMed id: 27383794 DOI: 10.1038/nature18622

Date:

07-Aug-15 Release date: 06-Jul-16

Protein chains

Q5SHR6  (RPOA_THET8) -  DNA-directed RNA polymerase subunit alpha from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 315 a.a.

Struc: 231 a.a.

Protein chains

Q8RQE9  (RPOB_THET8) -  DNA-directed RNA polymerase subunit beta from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1119 a.a.

Struc: 1112 a.a.

Protein chains

Q8RQE8  (RPOC_THET8) -  DNA-directed RNA polymerase subunit beta' from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 1524 a.a.

Struc: 1486 a.a.

Protein chains

Q8RQE7  (RPOZ_THET8) -  DNA-directed RNA polymerase subunit omega from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 99 a.a.

Struc: 94 a.a.

Protein chains

Q5SKW1  (Q5SKW1_THET8) -  RNA polymerase sigma factor SigA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 423 a.a.

Struc: 346 a.a.

DNA/RNA chains

G-C-A-T-C-C-G-T-G-A-G-T-A-G-A 15 bases

T-A-T-A-A-T-G-G-G-A-G-C-A-C-G-G-A-T-G-C 20 bases

G-C-A-T-C-C-G-T-G-A-G-T-A-G-A 15 bases

T-A-T-A-A-T-G-G-G-C-A-C-G-G-A-T-G-C 18 bases

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, K, L, M, N, O: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n) + ribonucleoside 5'-triphosphate = RNA(n+1) (Bound ligand (Het Group name = CTP) corresponds exactly) + diphosphate

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

Added reference

DOI no: 10.1038/nature18622

Nature 535:444-447 (2016)

PubMed id: 27383794

The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA.

J.G.Bird, Y.Zhang, Y.Tian, N.Panova, I.Barvík, L.Greene, M.Liu, B.Buckley, L.Krásný, J.K.Lee, C.D.Kaplan, R.H.Ebright, B.E.Nickels.

ABSTRACT

No abstract given.