Protein profile

KP13_01033

tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC

Genome: KpKP13

Gene: AHE43439.1 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
KP13_01033
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE43439.1 mnmC
Status
annotated
Amino acids
662
Structure source
AlphaFold + ColabFold
GO
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: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:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. 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: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 (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.3

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 0.664 · Pocket 22
P2Rank 0.986 · 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: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: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:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • 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: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
9 250 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
9 250 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
348 566 Gene3D G3DSA:3.30.9.10 -
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
267 628 Pfam PF01266 FAD dependent oxidoreductase
267 628 InterPro IPR006076 FAD dependent oxidoreductase
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
262 658 PANTHER PTHR13847 SARCOSINE DEHYDROGENASE-RELATED
118 244 Pfam PF05430 S-adenosyl-L-methionine-dependent methyltransferase
118 244 InterPro IPR008471 MnmC-like methyltransferase
9 249 FunFam G3DSA:3.40.50.150:FF:000107 tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
267 655 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
267 655 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
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
265 655 Gene3D G3DSA:3.50.50.60 -
265 655 InterPro IPR036188 FAD/NAD(P)-binding domain 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 KP13_01033
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