PDBsum entry 3n4m

Gene regulation/DNA

PDB id: 3n4m

Contents

Protein chains

203 a.a.

74 a.a.

DNA/RNA

Ligands

CMP ×2

PEG ×2

Waters ×35

PDB id:

3n4m

Name:

Gene regulation/DNA

Title:

E. Coli RNA polymerase alpha subunit c-terminal domain in complex with cap and DNA

Structure:

Catabolite gene activator. Chain: a. Synonym: camp receptor protein, camp regulatory protein. Engineered: yes. DNA-directed RNA polymerase subunit alpha. Chain: b, c. Fragment: alpha subunit c-terminal domain, residues 246-329. Synonym: rnap subunit alpha, transcriptase subunit alpha, RNA polymerase subunit alpha.

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: b3357, cap, crp, csm, jw5702. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: b3295, jw3257, pez, phs, rpoa, sez. Synthetic: yes. Synthetic: yes

Resolution:

2.99Å R-factor: 0.199 R-free: 0.224

Authors:

S.Lara-Gonzalez,J.J.Birktoft,C.L.Lawson

Key ref:

S.Lara-Gonzalez et al. (2020). The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Biochemistry, 59, 4523-4532. PubMed id: 33205945 DOI: 10.1021/acs.biochem.0c00571

Date:

21-May-10 Release date: 25-May-11

Protein chain

P0ACJ8  (CRP_ECOLI) -  DNA-binding transcriptional dual regulator CRP from Escherichia coli (strain K12)

Seq: 210 a.a.

Struc: 203 a.a.

Protein chains

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

Seq: 329 a.a.

Struc: 74 a.a.

DNA/RNA chains

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

C-T-A-G-A-T-C-A-C-A-T-T-T-T-A-G-G-A-A-A-A-A-A-G 24 bases

Enzyme reactions

• Enzyme class: Chains B, C: 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: 10.1021/acs.biochem.0c00571

Biochemistry 59:4523-4532 (2020)

PubMed id: 33205945

The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element.

S.Lara-Gonzalez, A.C.Dantas Machado, S.Rao, A.A.Napoli, J.Birktoft, R.Di Felice, R.Rohs, C.L.Lawson.

ABSTRACT

We demonstrate here that the α subunit C-terminal domain of Escherichia coli RNA polymerase (αCTD) recognizes the upstream promoter (UP) DNA element via its characteristic minor groove shape and electrostatic potential. In two compositionally distinct crystallized assemblies, a pair of αCTD subunits bind in tandem to the UP element consensus A-tract that is 6 bp in length (A₆-tract), each with their arginine 265 guanidinium group inserted into the minor groove. The A₆-tract minor groove is significantly narrowed in these crystal structures, as well as in computationally predicted structures of free and bound DNA duplexes derived by Monte Carlo and molecular dynamics simulations, respectively. The negative electrostatic potential of free A₆-tract DNA is substantially enhanced compared to that of generic DNA. Shortening the A-tract by 1 bp is shown to "knock out" binding of the second αCTD through widening of the minor groove. Furthermore, in computationally derived structures with arginine 265 mutated to alanine in either αCTD, either with or without the "knockout" DNA mutation, contact with the DNA is perturbed, highlighting the importance of arginine 265 in achieving αCTD-DNA binding. These results demonstrate that the importance of the DNA shape in sequence-dependent recognition of DNA by RNA polymerase is comparable to that of certain transcription factors.