Protein profile

VK055_3298

oxygen-independent coproporphyrinogen III oxidase

Genome: KpATCC43816

Gene: hemN AIK81859.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLB3
Export view
Amino acids 457
Annotations 10
Features 27
PDB binders 0
Druggability 0.655

Overview

Basic information about this protein and its source genome.

Accession
VK055_3298
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
hemN AIK81859.1
Status
annotated
Amino acids
457
Structure source
AlphaFold + ColabFold
EC
1.3.98.3
GO
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:0004109 Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX. GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.34
Human E-value
7.85e-23
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
47.788
DEG E-value
1.31e-146
Localization
Cytoplasmic
ColabFold pLDDT
96.13

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 0.655
Structure A0A0H3GLB3
Pocket Pocket 1
P2Rank 0.983
Structure A0A0H3GLB3
Pocket Pocket 1
ColabFold model
FPocket 0.73 · Pocket 27
P2Rank 0.982 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 155 / 4744 genomes with a hit
Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0004109 Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX.
  • GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0051989 Catalysis of the reaction: coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine.
  • GO:0046872 Binding to a metal ion.
  • GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
4 457 SFLD SFLDF00277 oxygen-independent coproporphyrinogen-III oxidase 1 (HemN-like)
4 457 InterPro IPR004558 Oxygen-independent coproporphyrinogen III oxidase HemN
52 270 Gene3D G3DSA:3.20.20.70 Aldolase class I
52 270 InterPro IPR013785 Aldolase-type TIM barrel
364 457 FunFam G3DSA:1.10.10.920:FF:000001 Coproporphyrinogen-III oxidase
60 280 FunFam G3DSA:3.80.30.20:FF:000012 Coproporphyrinogen-III oxidase
62 297 SFLD SFLDG01082 B12-binding domain containing
57 226 Pfam PF04055 Radical SAM superfamily
57 226 InterPro IPR007197 Radical SAM
8 445 PANTHER PTHR13932 COPROPORPHYRINIGEN III OXIDASE
8 445 InterPro IPR034505 Anaerobic coproporphyrinogen-III oxidase
62 274 CDD cd01335 Radical_SAM
50 278 FunFam G3DSA:3.20.20.70:FF:000077 Coproporphyrinogen-III oxidase
364 457 Gene3D G3DSA:1.10.10.920 -
4 457 SFLD SFLDS00029 Radical SAM
4 457 InterPro IPR007197 Radical SAM
6 457 NCBIfam TIGR00538 oxygen-independent coproporphyrinogen III oxidase
6 457 InterPro IPR004558 Oxygen-independent coproporphyrinogen III oxidase HemN
52 272 SMART SM00729 MiaB
52 272 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
363 431 Pfam PF06969 HemN C-terminal domain
363 431 InterPro IPR010723 HemN, C-terminal
2 454 PIRSF PIRSF000167 HemN
2 454 InterPro IPR004558 Oxygen-independent coproporphyrinogen III oxidase HemN
5 444 SUPERFAMILY SSF102114 Radical SAM enzymes
47 280 ProSiteProfiles PS51918 Radical SAM core domain profile.
47 280 InterPro IPR007197 Radical SAM

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_A0A0H3GLB3
AlphaFold — — full sequence — Viewing
ColabFold VK055_3298
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
1 0.655
2 0.021
4 0.005
22 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 61.63 0.983
2 20.09 0.788
3 7.03 0.304
4 2.57 0.059