Protein profile

VK055_3865

RNA polymerase sigma-54 factor

Genome: KpATCC43816

Gene: AIK82415.1 rpoN Structure source: Experimental + ColabFold UniProt A0A0H3H3L1|A0A0N9UTC1
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Amino acids 477
Annotations 4
Features 30
PDB binders 0
Druggability 0.954

Overview

Basic information about this protein and its source genome.

Accession
VK055_3865
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82415.1 rpoN
Status
annotated
Amino acids
477
Structure source
Experimental + ColabFold
GO
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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
89.937
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
81.48

Selected Druggability evidence

PDB experimental structure

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 0.954
Structure 7QWP
Pocket Pocket 1
P2Rank 0.104
Structure 7QXI
Pocket Pocket 1
ColabFold model
FPocket 0.607 · Pocket 3
P2Rank 0.042 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 132 / 4744 genomes with a hit
Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • 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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
1 476 PANTHER PTHR32248 RNA POLYMERASE SIGMA-54 FACTOR
1 476 InterPro IPR000394 RNA polymerase sigma factor 54
364 383 ProSitePatterns PS00717 Sigma-54 factors family signature 1.
364 383 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
121 193 Gene3D G3DSA:1.10.10.1330 -
121 193 InterPro IPR038709 RNA polymerase sigma-54 factor, core-binding domain superfamily
9 474 NCBIfam TIGR02395 RNA polymerase factor sigma-54
9 474 InterPro IPR000394 RNA polymerase sigma factor 54
1 477 PIRSF PIRSF000774 RpoN
1 477 InterPro IPR000394 RNA polymerase sigma factor 54
410 474 Gene3D G3DSA:1.10.10.60 -
317 475 Pfam PF04552 Sigma-54, DNA binding domain
317 475 InterPro IPR007634 RNA polymerase sigma factor 54, DNA-binding
116 303 Pfam PF04963 Sigma-54 factor, core binding domain
116 303 InterPro IPR007046 RNA polymerase sigma factor 54, core-binding domain
455 462 ProSitePatterns PS00718 Sigma-54 factors family signature 2.
455 462 InterPro IPR000394 RNA polymerase sigma factor 54
328 454 ProSiteProfiles PS50044 Sigma-54 factors family profile.
410 474 FunFam G3DSA:1.10.10.60:FF:000045 RNA polymerase sigma-54 factor
186 203 PRINTS PR00045 Sigma-54 factor signature
186 203 InterPro IPR000394 RNA polymerase sigma factor 54
376 388 PRINTS PR00045 Sigma-54 factor signature
376 388 InterPro IPR000394 RNA polymerase sigma factor 54
450 468 PRINTS PR00045 Sigma-54 factor signature
450 468 InterPro IPR000394 RNA polymerase sigma factor 54
392 403 PRINTS PR00045 Sigma-54 factor signature
392 403 InterPro IPR000394 RNA polymerase sigma factor 54
121 193 FunFam G3DSA:1.10.10.1330:FF:000001 RNA polymerase sigma-54 factor

3D Structure

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

3D visualization script Full viewer

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Structural evidence

2 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 7QWP
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Viewing
PDB 7QXI
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Loaded
ColabFold VK055_3865
ColabFold — — full sequence — Loaded
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
294 0.976
288 0.828
284 0.705
258 0.458