PDBsum entry 5byh

Transferase

PDB id: 5byh

Contents

Protein chains

305 a.a.

216 a.a.

1319 a.a.

1372 a.a.

79 a.a.

421 a.a.

Metals

_ZN

PDB id:

5byh

Name:

Transferase

Title:

Crystal structure of escherichia coli RNA polymerase - sigma54 holoenzyme complex

Structure:

DNA-directed RNA polymerase subunit alpha. Chain: a, b. Synonym: rnap subunit alpha,RNA polymerase subunit alpha, transcriptase subunit alpha. Engineered: yes. DNA-directed RNA polymerase subunit beta. Chain: c. Synonym: rnap subunit beta,RNA polymerase subunit beta,transcriptase subunit beta.

Source:

Escherichia coli (strain k12). Organism_taxid: 83333. Strain: k12. Gene: rpoa, faz83_23195. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768. Gene: rpob, gron, nitb, rif, ron, stl, stv, tabd, b3987, jw3950. Gene: rpoc, tabb, b3988, jw3951. Gene: rpoz, b3649, jw3624.

Resolution:

3.76Å R-factor: 0.347 R-free: 0.353

Authors:

X.Zhang,M.Buck,V.C.Darbari,Y.Yang,N.Zhang,D.Lu,R.Glyde,Y.Wang, J.Winkelman,R.L.Gourse,K.S.Murakami

Key ref:

Y.Yang et al. (2015). TRANSCRIPTION. Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies. Science, 349, 882-885. PubMed id: 26293966 DOI: 10.1126/science.aab1478

Date:

10-Jun-15 Release date: 02-Sep-15

Protein chain

A0A4S5AL01  (A0A4S5AL01_ECOLI) -

Protein chain

A0A4S5AL01  (A0A4S5AL01_ECOLI) -

Protein chain

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

Seq: 1342 a.a.

Struc: 1319 a.a.

Protein chain

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

Seq: 1407 a.a.

Struc: 1372 a.a.

Protein chain

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

Seq: 91 a.a.

Struc: 79 a.a.

Protein chain

A0A0N9UTC1  () -  RNA polymerase sigma-54 factor from Klebsiella pneumoniae

Seq: 477 a.a.

Struc: 421 a.a.

Enzyme reactions

• Enzyme class: Chains A, C, D, E: 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: 10.1126/science.aab1478

Science 349:882-885 (2015)

PubMed id: 26293966

TRANSCRIPTION. Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies.

Y.Yang, V.C.Darbari, N.Zhang, D.Lu, R.Glyde, Y.P.Wang, J.T.Winkelman, R.L.Gourse, K.S.Murakami, M.Buck, X.Zhang.

ABSTRACT

Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by σ factors. The major variant σ factor (σ(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activators for initiation. Our crystal structure of the 450-kilodalton RNAP-σ(54) holoenzyme at 3.8 angstroms reveals molecular details of σ(54) and its interactions with RNAP. The structure explains how σ(54) targets different regions in RNAP to exert its inhibitory function. Although σ(54) and the major σ factor, σ(70), have similar functional domains and contact similar regions of RNAP, unanticipated differences are observed in their domain arrangement and interactions with RNAP, explaining their distinct properties. Furthermore, we observe evolutionarily conserved regulatory hotspots in RNAPs that can be targeted by a diverse range of mechanisms to fine tune transcription.