PDBsum entry 6tqn

Transcription

PDB id: 6tqn

Contents

Protein chains

255 a.a.

495 a.a.

134 a.a.

98 a.a.

178 a.a.

322 a.a.

222 a.a.

90 a.a.

1342 a.a.

1337 a.a.

DNA/RNA

Metals

_MG ×3

_ZN ×2

PDB id:

6tqn

Name:

Transcription

Title:

Rrn anti-termination complex without s4

Structure:

Inositol monophosphatase. Chain: t. Engineered: yes. Inositol-1-monophosphatase. Chain: s. Synonym: inositol-1-phosphatase. Engineered: yes. Transcription termination/antitermination protein nusa. Chain: a.

Source:

Escherichia coli. Organism_taxid: 562. Gene: b9s25_006930. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: suhb, ssya, b2533, jw2517. Gene: nusa, ccu01_003250. Gene: nusb, ccu01_023355. Gene: rpsj, ad31_3986.

Authors:

Y.H.Huang,M.C.Wahl,B.Loll,T.Hilal,N.Said

Key ref:

Y.H.Huang et al. (2020). Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis. Mol Cell, 79, 1024. PubMed id: 32871103 DOI: 10.1016/j.molcel.2020.08.010

Date:

17-Dec-19 Release date: 05-Aug-20

Protein chains

P0ADG4  (SUHB_ECOLI) -  Nus factor SuhB from Escherichia coli (strain K12)

Seq: 267 a.a.

Struc: 255 a.a.

Protein chain

P0AFF6  (NUSA_ECOLI) -  Transcription termination/antitermination protein NusA from Escherichia coli (strain K12)

Seq: 495 a.a.

Struc: 495 a.a.*

Protein chain

P0A780  (NUSB_ECOLI) -  Transcription antitermination protein NusB from Escherichia coli (strain K12)

Seq: 139 a.a.

Struc: 134 a.a.

Protein chain

P0A7R5  (RS10_ECOLI) -  Small ribosomal subunit protein uS10 from Escherichia coli (strain K12)

Seq: 103 a.a.

Struc: 98 a.a.

Protein chain

P0AFG0  (NUSG_ECOLI) -  Transcription termination/antitermination protein NusG from Escherichia coli (strain K12)

Seq: 181 a.a.

Struc: 178 a.a.

Protein chain

P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha from Escherichia coli (strain K12)

Seq: 329 a.a.

Struc: 322 a.a.

Protein chain

P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha from Escherichia coli (strain K12)

Seq: 329 a.a.

Struc: 222 a.a.

Protein chain

P0A800  (RPOZ_ECOLI) -  DNA-directed RNA polymerase subunit omega from Escherichia coli (strain K12)

Seq: 91 a.a.

Struc: 90 a.a.

Protein chain

P0A8V2  (RPOB_ECOLI) -  DNA-directed RNA polymerase subunit beta from Escherichia coli (strain K12)

Seq: 1342 a.a.

Struc: 1342 a.a.

Protein chain

P0A8T7  (RPOC_ECOLI) -  DNA-directed RNA polymerase subunit beta' from Escherichia coli (strain K12)

Seq: 1407 a.a.

Struc: 1337 a.a.

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

DNA/RNA chains

A-C-U-G-C-U-C-U-U-U-A-A-C-A-A-U-U-U-A-U-C-A-G-A-U-C-U-G-U-G-U-G-G-G-U-G-G-C-G- 45 bases

G-T-T-A-T-C-C-G-C-T-C-A-C-A-A-T-G-C-C-A-C-A-C-G-C-G-C-T-G-C-T-C-G-G 34 bases

C-C-G-A-G-C-A-G-C-A-T-A-C-A-T-T-A-C-T-T-G-T-G-A-G-C-G-G-A-T-A-A-C 33 bases

Enzyme reactions

• Enzyme class 1: Chains T, S: E.C.3.1.3.25 - inositol-phosphate phosphatase.
• Pathway: myo-Inositol Biosynthesis
• Reaction: a myo-inositol phosphate + H2O = myo-inositol + phosphate
• Enzyme class 2: Chains U, V, W, X, Y: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

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

reference

DOI no: 10.1016/j.molcel.2020.08.010

Mol Cell 79:1024 (2020)

PubMed id: 32871103

Structure-Based Mechanisms of a Molecular RNA Polymerase/Chaperone Machine Required for Ribosome Biosynthesis.

Y.H.Huang, T.Hilal, B.Loll, J.Bürger, T.Mielke, C.Böttcher, N.Said, M.C.Wahl.

ABSTRACT

Bacterial ribosomal RNAs are synthesized by a dedicated, conserved transcription-elongation complex that transcribes at high rates, shields RNA polymerase from premature termination, and supports co-transcriptional RNA folding, modification, processing, and ribosomal subunit assembly by presently unknown mechanisms. We have determined cryo-electron microscopy structures of complete Escherichia coli ribosomal RNA transcription elongation complexes, comprising RNA polymerase; DNA; RNA bearing an N-utilization-site-like anti-termination element; Nus factors A, B, E, and G; inositol mono-phosphatase SuhB; and ribosomal protein S4. Our structures and structure-informed functional analyses show that fast transcription and anti-termination involve suppression of NusA-stabilized pausing, enhancement of NusG-mediated anti-backtracking, sequestration of the NusG C-terminal domain from termination factor ρ, and the ρ blockade. Strikingly, the factors form a composite RNA chaperone around the RNA polymerase RNA-exit tunnel, which supports co-transcriptional RNA folding and annealing of distal RNA regions. Our work reveals a polymerase/chaperone machine required for biosynthesis of functional ribosomes.