Protein profile

KP13_01819

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase

Genome: KpKP13

Gene: AHE46259.1 mtnN Structure source: Experimental + ColabFold UniProt A6T4W3
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Amino acids 232
Annotations 6
Features 12
PDB binders 11
Druggability 0.374

Overview

Basic information about this protein and its source genome.

Accession
KP13_01819
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE46259.1 mtnN
Status
annotated
Amino acids
232
Structure source
Experimental + ColabFold
GO
GO:0009164 The chemical reactions and pathways resulting in the breakdown of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside). GO:0009116 The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine). GO:0008782 Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenine + S-D-ribosyl-L-homocysteine. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0019509 OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine. GO:0008930 Catalysis of the reaction: methylthioadenosine + H2O = adenine + 5-methylthio-D-ribose.

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 (%)
90.517
DEG E-value
2.31e-148
Localization
Cytoplasmic
ColabFold pLDDT
95.69

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 0.374
Structure 4G89
Pocket Pocket 2
P2Rank 0.357
Structure 4G89
Pocket Pocket 1
ColabFold model
FPocket 0.766 · Pocket 1
P2Rank 0.47 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 195 / 4744 genomes with a hit
Normalized 0.041

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0009164 The chemical reactions and pathways resulting in the breakdown of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
  • GO:0009116 The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
  • GO:0008782 Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenine + S-D-ribosyl-L-homocysteine.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0019509 OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
  • GO:0008930 Catalysis of the reaction: methylthioadenosine + H2O = adenine + 5-methylthio-D-ribose.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
2 229 Hamap MF_01684 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase [mtnN].
2 229 InterPro IPR010049 MTA/SAH nucleosidase
2 225 Pfam PF01048 Phosphorylase superfamily
2 225 InterPro IPR000845 Nucleoside phosphorylase domain
2 229 PANTHER PTHR46832 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE
1 230 FunFam G3DSA:3.40.50.1580:FF:000001 MTA/SAH nucleosidase family protein
1 232 Gene3D G3DSA:3.40.50.1580 Nucleoside phosphorylase domain
1 232 InterPro IPR035994 Nucleoside phosphorylase superfamily
3 225 CDD cd09008 MTAN
2 229 NCBIfam TIGR01704 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
1 229 SUPERFAMILY SSF53167 Purine and uridine phosphorylases
1 229 InterPro IPR035994 Nucleoside phosphorylase superfamily

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

1 + 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 4G89
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Viewing
ColabFold KP13_01819
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 0.868

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 12.52 0.654
2 11.84 0.627
3 7.46 0.392
4 5.88 0.287
5 5.15 0.237

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

95 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
ADE
4G89 Open crystal
135.1 Da LogP -0.06 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.