Protein profile

VK055_4799

tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain

Genome: KpATCC43816

Gene: AIK83326.1 mnmC Structure source: AlphaFold + ColabFold UniProt A0A0H3GWE4
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Amino acids 662
Annotations 9
Features 22
PDB binders 0
Druggability 0.867

Overview

Basic information about this protein and its source genome.

Accession
VK055_4799
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83326.1 mnmC
Status
annotated
Amino acids
662
Structure source
AlphaFold + ColabFold
GO
GO:0004808 Catalysis of the reaction: 5-aminomethyl-2-thiouridine34 in tRNA + S-adenosyl-L-methionine = 5-methylaminomethyl-2-thiouridine34 in tRNA + H+ + S-adenosyl-L-homocysteine. This enzyme specifically adds the terminal methyl group of 5-[(methylamino)methyl]-2-thiouridylate. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0016645 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
50.279
Localization
Cytoplasmic
ColabFold pLDDT
96.24

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 0.867
Structure A0A0H3GWE4
Pocket Pocket 3
P2Rank 0.983
Structure A0A0H3GWE4
Pocket Pocket 1
ColabFold model
FPocket 0.721 · Pocket 1
P2Rank 0.984 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

9
  • GO:0004808 Catalysis of the reaction: 5-aminomethyl-2-thiouridine34 in tRNA + S-adenosyl-L-methionine = 5-methylaminomethyl-2-thiouridine34 in tRNA + H+ + S-adenosyl-L-homocysteine. This enzyme specifically adds the terminal methyl group of 5-[(methylamino)methyl]-2-thiouridylate.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0016645 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
267 628 Pfam PF01266 FAD dependent oxidoreductase
267 628 InterPro IPR006076 FAD dependent oxidoreductase
118 244 Pfam PF05430 S-adenosyl-L-methionine-dependent methyltransferase
118 244 InterPro IPR008471 MnmC-like methyltransferase
267 655 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
267 655 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
9 250 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
9 250 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
267 658 NCBIfam TIGR03197 FAD-dependent 5-carboxymethylaminomethyl-2-thiouridine(34) oxidoreductase MnmC
267 658 InterPro IPR017610 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC, C-terminal
472 548 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain
348 566 Gene3D G3DSA:3.30.9.10 -
7 653 Hamap MF_01102 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC [mnmC].
7 653 InterPro IPR023032 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
262 658 PANTHER PTHR13847 SARCOSINE DEHYDROGENASE-RELATED
9 249 FunFam G3DSA:3.40.50.150:FF:000107 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
19 243 NCBIfam NF033855 tRNA (5-methylaminomethyl-2-thiouridine)(34)-methyltransferase MnmD
19 243 InterPro IPR047785 tRNA mnm(5)s(2)U biosynthesis bifunctional protein MnmC, N-terminal
265 655 Gene3D G3DSA:3.50.50.60 -
265 655 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
62 239 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
62 239 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

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_A0A0H3GWE4
AlphaFold — — full sequence — Viewing
ColabFold VK055_4799
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
3 0.867
15 0.725

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 34.32 0.95
2 19.55 0.841
3 3.25 0.113
4 3.15 0.107