Protein profile

PA4462

RNA polymerase factor sigma-54

Genome: NC_002516.2

Gene: PA4462 rpoN Structure source: AlphaFold UniProt P49988
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Amino acids 497
Annotations 10
Features 33
PDB binders 0
Druggability 0.509

Overview

Basic information about this protein and its source genome.

Accession
PA4462
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4462 rpoN
Status
annotated
Amino acids
497
Structure source
AlphaFold
GO
GO:0000428 A protein complex that possesses DNA-directed RNA polymerase activity. GO:0032993 A macromolecular complex containing both protein and DNA molecules. GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets. GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor). GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins. GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.509
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Gene Ontology (GO)

10
  • GO:0000428 A protein complex that possesses DNA-directed RNA polymerase activity.
  • GO:0032993 A macromolecular complex containing both protein and DNA molecules.
  • GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
  • GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
  • GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
  • GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
  • GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
  • GO:1900191 Any process that stops, prevents or reduces the frequency, rate or extent of single-species biofilm formation.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
348 474 ProSiteProfiles PS50044 Sigma-54 factors family profile.
475 482 ProSitePatterns PS00718 Sigma-54 factors family signature 2.
475 482 InterPro IPR000394 RNA polymerase sigma factor 54
5 48 Pfam PF00309 Sigma-54 factor, Activator interacting domain (AID)
5 48 InterPro IPR000394 RNA polymerase sigma factor 54
430 494 Gene3D G3DSA:1.10.10.60 -
129 323 Pfam PF04963 Sigma-54 factor, core binding domain
129 323 InterPro IPR007046 RNA polymerase sigma factor 54, core-binding domain
384 403 ProSitePatterns PS00717 Sigma-54 factors family signature 1.
384 403 InterPro IPR000394 RNA polymerase sigma factor 54
140 213 Gene3D G3DSA:1.10.10.1330 -
140 213 InterPro IPR038709 RNA polymerase sigma-54 factor, core-binding domain superfamily
252 272 Coils Coil Coil
72 89 MobiDBLite mobidb-lite consensus disorder prediction
1 496 PANTHER PTHR32248 RNA POLYMERASE SIGMA-54 FACTOR
1 496 InterPro IPR000394 RNA polymerase sigma factor 54
10 494 NCBIfam TIGR02395 RNA polymerase factor sigma-54
10 494 InterPro IPR000394 RNA polymerase sigma factor 54
412 423 PRINTS PR00045 Sigma-54 factor signature
412 423 InterPro IPR000394 RNA polymerase sigma factor 54
396 408 PRINTS PR00045 Sigma-54 factor signature
396 408 InterPro IPR000394 RNA polymerase sigma factor 54
470 488 PRINTS PR00045 Sigma-54 factor signature
470 488 InterPro IPR000394 RNA polymerase sigma factor 54
206 223 PRINTS PR00045 Sigma-54 factor signature
206 223 InterPro IPR000394 RNA polymerase sigma factor 54
39 100 MobiDBLite mobidb-lite consensus disorder prediction
337 495 Pfam PF04552 Sigma-54, DNA binding domain
337 495 InterPro IPR007634 RNA polymerase sigma factor 54, DNA-binding
430 494 FunFam G3DSA:1.10.10.60:FF:000045 RNA polymerase sigma-54 factor
140 213 FunFam G3DSA:1.10.10.1330:FF:000001 RNA polymerase sigma-54 factor
1 497 PIRSF PIRSF000774 RpoN
1 497 InterPro IPR000394 RNA polymerase sigma factor 54

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

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Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4462
AlphaFold — — full sequence — Viewing
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.509
5 0.25
2 0.206