Bacterial DNA-directed RNA polymerase core enzyme

Species-neutral bacterial module for the DNA-directed RNA polymerase core enzyme that carries out DNA-templated RNA synthesis. The conserved bacterial core enzyme is built from an alpha dimer, beta and beta-prime catalytic cleft subunits, and the omega assembly/stability subunit. This module deliberately stops at the core enzyme and excludes sigma factors, transcription elongation factors, and promoter-specific regulatory proteins.

MODULE:bacterial_rna_polymerase_coreDRAFTCONCRETEProtein Complexmodules/bacterial_rna_polymerase_core.yaml
DNA-directed RNA polymerase complexGO:0000428 DNA-templated transcriptionGO:0006351
KEGG:ppu03020
Pseudomonas putida KT2440 RNA polymerase
The local PSEPK pathway partition assigns rpoA, rpoB, rpoC, and rpoZ as the four primary genes in the compact KEGG ppu03020 RNA polymerase bucket.
GO:0000428
DNA-directed RNA polymerase complex
UniProt records for the PSEPK rpoA, rpoB, rpoC, and rpoZ exemplars all carry GO:0000428, supporting this module as a protein-complex module rather than a linear metabolic pathway.
GO:0003899
DNA-directed RNA polymerase activity
GO:0003899 captures the complex-level nucleotidyltransferase activity performed by the assembled core enzyme during transcription.
file:PSEPK/rpoA/rpoA-uniprot.txt
UniProtKB entry for PSEPK rpoA
Q88QL1 is the P. putida KT2440 DNA-directed RNA polymerase alpha subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, dimerization, and DNA-templated transcription annotations.
file:PSEPK/rpoB/rpoB-uniprot.txt
UniProtKB entry for PSEPK rpoB
Q88QP2 is the P. putida KT2440 DNA-directed RNA polymerase beta subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, ribonucleoside binding, and DNA-templated transcription annotations.
file:PSEPK/rpoC/rpoC-uniprot.txt
UniProtKB entry for PSEPK rpoC
Q88QP1 is the P. putida KT2440 DNA-directed RNA polymerase beta-prime subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, magnesium and zinc ion binding, and DNA-templated transcription annotations.
file:PSEPK/rpoZ/rpoZ-uniprot.txt
UniProtKB entry for PSEPK rpoZ
Q88C82 is the P. putida KT2440 DNA-directed RNA polymerase omega subunit and carries RNA polymerase complex, DNA binding, RNA polymerase activity, and DNA-templated transcription annotations.

First-pass PSEPK interpretation: rpoA, rpoB, rpoC, and rpoZ satisfy the core RNA polymerase enzyme module. Sigma factors such as RpoD, RpoN, RpoS, RpoH, RpoE, FliA, and ECF sigma factors should be curated in promoter-recognition or stress-response modules, not as required parts of this core-enzyme module.

4Nodes
3Parts
0Variant Sets
0Variants
4Annotons
2Connections

Derived QC

Recommended-field compliance

60.0% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)

Module deep research

✓ present

  • bacterial_rna_polymerase_core-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (4/4 grounded genes reviewed)

4 complete review(s) · 2 with deep research · 0 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
rpoA Q88QL1 ✓ ✓ ✓
rpoB Q88QP2 ✓ ✓ ✗
rpoC Q88QP1 ✓ ✓ ✓
rpoZ Q88C82 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
cytosolGO:0005829
Bacterial DNA-directed RNA polymerase core enzymeProtein Complexbacterial_rna_polymerase_core
DNA-directed RNA polymerase complexGO:0000428 DNA-templated transcriptionGO:0006351
Context
bacteriaNCBITaxon:2
cytosolGO:0005829

Connections

The alpha dimer provides the assembly platform for recruitment of the beta and beta-prime subunits into the core enzyme.
The omega subunit supports proper assembly and stability of the beta/beta-prime-containing core enzyme.
Part 1: alpha dimer assembly platform
RpoA alpha dimer platformProtein Complexrpoa_alpha_dimer_platform

The alpha subunit forms the dimeric assembly platform that nucleates core enzyme assembly and contributes to DNA/promoter contacts.

Annotons

rpoA: RNA polymerase alpha subunit
rpoa_alpha_subunit
Participant: Family: bacterial DNA-directed RNA polymerase alpha subunit family
Family:
bacterial DNA-directed RNA polymerase alpha subunit familyInterPro:IPR011773
Representative Members: PSEPK rpoA exemplarUniProtKB:Q88QL1

Function

protein dimerization activityGO:0046983

Processes

DNA-templated transcriptionGO:0006351

Locations

cytosolGO:0005829

Alpha subunit that dimerizes and forms the scaffold for beta and beta-prime subunit recruitment in the bacterial core enzyme.

Part 2: beta and beta-prime catalytic cleft
RpoB/RpoC catalytic cleftProtein Complexrpob_rpoc_catalytic_cleft

The beta and beta-prime subunits form the active-center cleft that binds DNA/RNA substrates, divalent metal ions, and incoming ribonucleotides for RNA-chain elongation.

Annotons

rpoB: RNA polymerase beta subunit
rpob_beta_subunit
Participant: Family: DNA-directed RNA polymerase beta subunit family
Family:
DNA-directed RNA polymerase beta subunit familyInterPro:IPR010243
Representative Members: PSEPK rpoB exemplarUniProtKB:Q88QP2

Function

contributes to DNA-directed RNA polymerase activityGO:0003899
Substrates: DNA template ribonucleoside triphosphates
Products: RNA transcript

Processes

DNA-templated transcriptionGO:0006351

Locations

cytosolGO:0005829

Beta subunit that helps form the catalytic cleft and contributes substrate-binding surfaces for RNA synthesis by the assembled core.

rpoC: RNA polymerase beta-prime subunit
rpoc_beta_prime_subunit
Participant: Family: bacterial DNA-directed RNA polymerase beta-prime subunit family
Family:
bacterial DNA-directed RNA polymerase beta-prime subunit familyInterPro:IPR012754
Representative Members: PSEPK rpoC exemplarUniProtKB:Q88QP1

Function

contributes to DNA-directed RNA polymerase activityGO:0003899
Substrates: DNA template ribonucleoside triphosphates
Products: RNA transcript
Cofactors: magnesium ionGO:0000287 zinc ionGO:0008270

Processes

DNA-templated transcriptionGO:0006351

Locations

cytosolGO:0005829

Beta-prime subunit that supplies core active-center architecture, metal-binding determinants, and DNA/RNA binding surfaces.

Part 3: omega assembly and stability subunit
RpoZ omega assembly/stability subunitProtein Complexrpoz_omega_assembly_subunit

The omega subunit is a small conserved RNA polymerase component that promotes proper core-enzyme assembly and stability.

Annotons

rpoZ: RNA polymerase omega subunit
rpoz_omega_subunit
Participant: Family: DNA-directed RNA polymerase omega subunit family
Family:
DNA-directed RNA polymerase omega subunit familyPANTHER:PTHR34476
Representative Members: PSEPK rpoZ exemplarUniProtKB:Q88C82

Function

contributes to DNA-directed RNA polymerase activityGO:0003899

Processes

DNA-templated transcriptionGO:0006351

Locations

cytosolGO:0005829

Small omega subunit that stabilizes and supports assembly of the bacterial RNA polymerase core enzyme.