Structure of E. coli RNA Polymerase

Subunits of E. coli RNA Polymerase:

• E. coli RNA polymerase has a unique crab claw-like shape, with a cylindrical channel that binds 16 base pairs of DNA.
• It covers a promoter region of about 60 base pairs, with 16 base pairs in the active site where transcription occurs.
• The enzyme requires magnesium ions and has a transcription rate of approximately 40 nucleotides per second at 37°C.
• RNA polymerase enzymes across different organisms share a crab claw-like structure with the active site located at the base of the largest subunits, which are essential for transcription.

Subunits of E. coli RNA Polymerase:

1. Beta' (B') Subunit:
   • Encoded by the rpoC gene, contains the active center for RNA synthesis, and interacts with DNA and RNA.
   • Binds two magnesium ions essential for catalysis and is inhibited by heparin in vitro.
2. Beta (B) Subunit:
   • Encoded by the rpoB gene, contains elements for interacting with DNA and RNA.
   • Targeted by antibiotics like Rifampicin and Streptolydigins that inhibit different stages of transcription.
3. Alpha Subunits:
   • Consist of N-terminal and C-terminal domains (CTD), with roles in enzyme assembly and interactions with promoter DNA and regulatory factors.
   • Can be modified by bacteriophage T4, affecting binding efficiency.
4. Omega Subunit:
   • Smallest subunit, crucial for the assembly and stability of the RNA polymerase complex.
5. Sigma Factor:
   • Associates with the core enzyme to form the holoenzyme, directing RNA polymerase to specific promoter regions for transcription initiation.
   • Detaches after initiation, allowing the core enzyme to elongate the RNA transcript.

Related Facts:

• Bacterial and yeast RNA polymerases share similar structures and organization.
• Antibiotics like Actinomycin D can block transcription in both E. coli and yeast due to their structural similarities.
• Archaeal RNA polymerase is similar to both bacterial RNA polymerase and eukaryotic RNA polymerases, particularly eukaryotic RNA Polymerase II.