Protein profile

VK055_4294

exodeoxyribonuclease V, gamma subunit

Genome: KpATCC43816

Gene: AIK82839.1 recC Structure source: AlphaFold + ColabFold UniProt A0A0H3GX23
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Amino acids 1109
Annotations 6
Features 29
PDB binders 0
Druggability 0.581

Overview

Basic information about this protein and its source genome.

Accession
VK055_4294
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82839.1 recC
Status
annotated
Amino acids
1109
Structure source
AlphaFold + ColabFold
GO
GO:0009338 An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA. GO:0008854 Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis. GO:0000724 The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.

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 (%)
78.391
DEG E-value
0.0
Localization
Unknown
ColabFold pLDDT
92.78

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 0.581
Structure A0A0H3GX23
Pocket Pocket 96
P2Rank 0.157
Structure A0A0H3GX23
Pocket Pocket 1
ColabFold model
FPocket 0.677 · Pocket 72
P2Rank 0.568 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 108 / 4744 genomes with a hit
Normalized 0.023

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:0009338 An enzyme complex that catalyzes exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides. Exodeoxyribonuclease V shows a preference for double-stranded DNA and possesses DNA-dependent ATPase activity. It acts endonucleolytically on single-stranded circular DNA.
  • GO:0008854 Catalysis of the exonucleolytic cleavage (in the presence of ATP) in either 5' to 3' or 3' to 5' direction to yield 5'-phosphooligonucleotides.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • GO:0000724 The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
1 1107 Hamap MF_01486 RecBCD enzyme subunit RecC [recC].
1 1107 InterPro IPR006697 RecBCD enzyme subunit RecC
346 796 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
346 796 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
591 795 FunFam G3DSA:3.40.50.300:FF:001153 RecBCD enzyme subunit RecC
70 169 Gene3D G3DSA:1.10.10.160 -
70 169 InterPro IPR013986 DExx box DNA helicase domain superfamily
70 169 FunFam G3DSA:1.10.10.160:FF:000003 RecBCD enzyme subunit RecC
3 235 Gene3D G3DSA:3.40.50.10930 -
804 1103 SUPERFAMILY SSF52980 Restriction endonuclease-like
804 1103 InterPro IPR011335 Restriction endonuclease type II-like
3 1107 PANTHER PTHR30591 RECBCD ENZYME SUBUNIT RECC
5 328 Pfam PF04257 Exodeoxyribonuclease V, gamma subunit
908 928 Coils Coil Coil
600 795 Gene3D G3DSA:3.40.50.300 -
600 795 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
311 461 Gene3D G3DSA:3.40.50.300 -
311 461 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 1108 PIRSF PIRSF000980 RecC
1 1108 InterPro IPR006697 RecBCD enzyme subunit RecC
6 331 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
6 331 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
818 1100 CDD cd22353 RecC_C-like
848 919 Gene3D G3DSA:1.10.10.990 -
2 1070 NCBIfam TIGR01450 exodeoxyribonuclease V subunit gamma
2 1070 InterPro IPR006697 RecBCD enzyme subunit RecC
311 466 FunFam G3DSA:3.40.50.300:FF:001068 RecBCD enzyme subunit RecC
815 1033 Pfam PF17946 RecC C-terminal domain
815 1033 InterPro IPR041500 RecC, C-terminal

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_A0A0H3GX23
AlphaFold — — full sequence — Viewing
ColabFold VK055_4294
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
5 0.205
64 0.104
97 0.002
102 0.002

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 4.48 0.157
2 4.27 0.145
3 3.74 0.115
4 2.92 0.075
5 2.87 0.073