Protein profile

VK055_3904

tRNA pseudouridine(55) synthase

Genome: KpATCC43816

Gene: AIK82452.1 truB Structure source: AlphaFold + ColabFold UniProt A0A0H3GTP1
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Amino acids 314
Annotations 9
Features 24
PDB binders 0
Druggability 0.398

Overview

Basic information about this protein and its source genome.

Accession
VK055_3904
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82452.1 truB
Status
annotated
Amino acids
314
Structure source
AlphaFold + ColabFold
EC
5.4.99.25
GO
GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0009451 The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0001522 The intramolecular conversion of uridine to pseudouridine within an RNA molecule. GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5. GO:0160148 Catalysis of the reaction: uridine(55) in tRNA = pseudouridine(55) in tRNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
41.509
Human E-value
4.56e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
59.322
DEG E-value
6.54e-120
Localization
Cytoplasmic
ColabFold pLDDT
94.6

Selected Druggability evidence

AlphaFold / UniProt model

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 0.398
Structure A0A0H3GTP1
Pocket Pocket 4
P2Rank 0.361
Structure A0A0H3GTP1
Pocket Pocket 1
ColabFold model
FPocket 0.555 · Pocket 9
P2Rank 0.33 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 150 / 4744 genomes with a hit
Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
  • GO:0009451 The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0001522 The intramolecular conversion of uridine to pseudouridine within an RNA molecule.
  • GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
  • GO:0160148 Catalysis of the reaction: uridine(55) in tRNA = pseudouridine(55) in tRNA.
  • GO:1990481 The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
  • GO:0031119 The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
252 309 Pfam PF09157 Pseudouridine synthase II TruB, C-terminal
252 309 InterPro IPR015240 tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal
11 309 Hamap MF_01080 tRNA pseudouridine synthase B [truB].
11 309 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
13 222 CDD cd02573 PseudoU_synth_EcTruB
13 222 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
12 219 NCBIfam TIGR00431 tRNA pseudouridine(55) synthase TruB
12 219 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
250 314 Gene3D G3DSA:2.30.130.10 PUA domain
250 314 InterPro IPR036974 PUA domain superfamily
250 314 FunFam G3DSA:2.30.130.10:FF:000004 tRNA pseudouridine synthase B
181 247 Pfam PF16198 tRNA pseudouridylate synthase B C-terminal domain
181 247 InterPro IPR032819 tRNA pseudouridylate synthase B, C-terminal
1 249 Gene3D G3DSA:3.30.2350.10 Pseudouridine synthase
251 310 SUPERFAMILY SSF88697 PUA domain-like
251 310 InterPro IPR015947 PUA-like superfamily
11 246 SUPERFAMILY SSF55120 Pseudouridine synthase
11 246 InterPro IPR020103 Pseudouridine synthase, catalytic domain superfamily
6 226 PANTHER PTHR13767 TRNA-PSEUDOURIDINE SYNTHASE
6 226 InterPro IPR014780 tRNA pseudouridine synthase II, TruB
33 180 Pfam PF01509 TruB family pseudouridylate synthase (N terminal domain)
33 180 InterPro IPR002501 Pseudouridine synthase II, N-terminal
1 249 FunFam G3DSA:3.30.2350.10:FF:000003 tRNA pseudouridine synthase B
249 309 CDD cd21152 PUA_TruB_bacterial

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

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GTP1
AlphaFold — — full sequence — Viewing
ColabFold VK055_3904
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
4 0.398
16 0.051
1 0.05
17 0.001

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 8.04 0.361
2 3.15 0.085
3 1.22 0.01