Protein profile

KP13_05628

Site-specific DNA-methyltransferase (cytosine-N4-specific)

Genome: KpKP13

Gene: AHE41907.1 Structure source: AlphaFold + ColabFold UniProt A0A210VJ13
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Amino acids 414
Annotations 8
Features 20
PDB binders 0
Druggability 0.434

Overview

Basic information about this protein and its source genome.

Accession
KP13_05628
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE41907.1
Status
annotated
Amino acids
414
Structure source
AlphaFold + ColabFold
EC
2.1.1.-
GO
GO:0090124 OBSOLETE. The covalent transfer of a methyl group to N-4 of cytosine in a DNA molecule. GO:0006306 OBSOLETE. The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. GO:0008170 Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule. GO:0015667 Catalysis of the reaction: S-adenosyl-L-methionine + DNA cytosine = S-adenosyl-L-homocysteine + DNA N4-methylcytosine. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0009307 A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.

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
88.13

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 0.434
Structure A0A210VJ13
Pocket Pocket 33
P2Rank 0.713
Structure A0A210VJ13
Pocket Pocket 1
ColabFold model
FPocket 0.864 · Pocket 1
P2Rank 0.859 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 5 / 4744 genomes with a hit
Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0090124 OBSOLETE. The covalent transfer of a methyl group to N-4 of cytosine in a DNA molecule.
  • GO:0006306 OBSOLETE. The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
  • GO:0008170 Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule.
  • GO:0015667 Catalysis of the reaction: S-adenosyl-L-methionine + DNA cytosine = S-adenosyl-L-homocysteine + DNA N4-methylcytosine.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0009307 A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
106 392 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
106 392 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
16 94 Pfam PF14338 Mrr N-terminal domain
16 94 InterPro IPR025745 Restriction system protein Mrr-like N-terminal domain
129 389 Pfam PF01555 DNA methylase
129 389 InterPro IPR002941 DNA methylase N-4/N-6
104 396 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
104 396 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
133 138 ProSitePatterns PS00093 N-4 cytosine-specific DNA methylases signature.
133 138 InterPro IPR017985 DNA methylase, N-4 cytosine-specific, conserved site
351 369 PRINTS PR00508 S21 class N4 adenine-specific DNA methyltransferase signature
351 369 InterPro IPR001091 Restriction/modification DNA-methyltransferase
128 142 PRINTS PR00508 S21 class N4 adenine-specific DNA methyltransferase signature
128 142 InterPro IPR001091 Restriction/modification DNA-methyltransferase
332 349 PRINTS PR00508 S21 class N4 adenine-specific DNA methyltransferase signature
332 349 InterPro IPR001091 Restriction/modification DNA-methyltransferase
374 394 PRINTS PR00508 S21 class N4 adenine-specific DNA methyltransferase signature
374 394 InterPro IPR001091 Restriction/modification DNA-methyltransferase
161 181 PRINTS PR00508 S21 class N4 adenine-specific DNA methyltransferase signature
161 181 InterPro IPR001091 Restriction/modification DNA-methyltransferase

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_A0A210VJ13
AlphaFold — — full sequence — Viewing
ColabFold KP13_05628
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
33 0.434
1 0.29

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 14.99 0.741
2 3.87 0.151
3 3.15 0.107
4 0.8 0.002