Protein profile

KP13_02392

7-carboxy-7-deazaguanine synthase-like protein

Genome: KpKP13

Gene: AHE42963.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSC0
Export view
Amino acids 223
Annotations 8
Features 18
PDB binders 0
Druggability 0.201

Overview

Basic information about this protein and its source genome.

Accession
KP13_02392
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42963.1
Status
annotated
Amino acids
223
Structure source
AlphaFold + ColabFold
EC
4.3.99.3
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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. 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:0016840 Catalysis of the release of ammonia or one of its derivatives, with the formation of a double bond or ring. Enzymes with this activity may catalyze the actual elimination of the ammonia, amine or amide, e.g. CH-CH(-NH-R) = C=CH- + NH2-R. Others, however, catalyze elimination of another component, e.g. water, which is followed by spontaneous reactions that lead to breakage of the C-N bond, e.g. L-serine ammonia-lyase (EC:4.3.1.17), so that the overall reaction is C(-OH)-CH(-NH2) = CH2-CO- + NH4+, i.e. an elimination with rearrangement. The sub-subclasses of EC:4.3 are the ammonia-lyases (EC:4.3.1), lyases acting on amides, amidines, etc. (EC:4.3.2), the amine-lyases (EC:4.3.3), and other carbon-nitrogen lyases (EC:4.3.99). GO:0000287 Binding to a magnesium (Mg) ion. GO:1904047 Binding to S-adenosyl-L-methionine.

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 (%)
91.928
DEG E-value
3.22e-159
Localization
Cytoplasmic
ColabFold pLDDT
95.96

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 0.201
Structure A0A0H3GSC0
Pocket Pocket 4
P2Rank 0.961
Structure A0A0H3GSC0
Pocket Pocket 1
ColabFold model
FPocket 0.14 · Pocket 1
P2Rank 0.96 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 119 / 4744 genomes with a hit
Normalized 0.025

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: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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • 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:0016840 Catalysis of the release of ammonia or one of its derivatives, with the formation of a double bond or ring. Enzymes with this activity may catalyze the actual elimination of the ammonia, amine or amide, e.g. CH-CH(-NH-R) = C=CH- + NH2-R. Others, however, catalyze elimination of another component, e.g. water, which is followed by spontaneous reactions that lead to breakage of the C-N bond, e.g. L-serine ammonia-lyase (EC:4.3.1.17), so that the overall reaction is C(-OH)-CH(-NH2) = CH2-CO- + NH4+, i.e. an elimination with rearrangement. The sub-subclasses of EC:4.3 are the ammonia-lyases (EC:4.3.1), lyases acting on amides, amidines, etc. (EC:4.3.2), the amine-lyases (EC:4.3.3), and other carbon-nitrogen lyases (EC:4.3.99).
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:1904047 Binding to S-adenosyl-L-methionine.
  • GO:0008616 The chemical reactions and pathways resulting in the formation of queuosines, a series of nucleosides found in position 34 of tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents. 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.

18 records
Show feature table
Start End DB Term Name
24 119 SUPERFAMILY SSF102114 Radical SAM enzymes
1 223 PIRSF PIRSF000370 QueE
1 223 InterPro IPR024924 7-carboxy-7-deazaguanine synthase-like
2 223 FunFam G3DSA:3.20.20.70:FF:000085 7-carboxy-7-deazaguanine synthase
2 223 Gene3D G3DSA:3.20.20.70 Aldolase class I
2 223 InterPro IPR013785 Aldolase-type TIM barrel
1 222 PANTHER PTHR42836 7-CARBOXY-7-DEAZAGUANINE SYNTHASE
27 183 Pfam PF04055 Radical SAM superfamily
27 183 InterPro IPR007197 Radical SAM
3 223 Hamap MF_00917 7-carboxy-7-deazaguanine synthase [queE].
3 223 InterPro IPR024924 7-carboxy-7-deazaguanine synthase-like
18 223 ProSiteProfiles PS51918 Radical SAM core domain profile.
18 223 InterPro IPR007197 Radical SAM
9 223 NCBIfam TIGR04322 7-carboxy-7-deazaguanine synthase QueE
9 223 InterPro IPR027609 7-carboxy-7-deazaguanine synthase, proteobacteria
26 183 SFLD SFLDS00029 Radical SAM
26 183 InterPro IPR007197 Radical SAM
24 127 Pfam PF13394 4Fe-4S single cluster domain

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_A0A0H3GSC0
AlphaFold — — full sequence — Viewing
ColabFold KP13_02392
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
4 0.201

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 30.95 0.937
2 1.55 0.023