Protein profile

KP13_01621

Holliday junction ATP-dependent DNA helicase ruvA

Genome: KpKP13

Gene: ruvA AHE43856.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ62
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Amino acids 203
Annotations 11
Features 27
PDB binders 0
Druggability 0.515

Overview

Basic information about this protein and its source genome.

Accession
KP13_01621
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ruvA AHE43856.1
Status
annotated
Amino acids
203
Structure source
AlphaFold + ColabFold
GO
GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis. GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. GO:0009379 A DNA helicase complex found at Holliday junctions where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA. GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. 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).

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 (%)
95.074
DEG E-value
3.34e-142
Localization
Cytoplasmic
ColabFold pLDDT
89.39

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 0.515
Structure A0A0H3GQ62
Pocket Pocket 11
P2Rank 0.032
Structure A0A0H3GQ62
Pocket Pocket 1
ColabFold model
FPocket 0.717 · Pocket 7
P2Rank 0.086 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 160 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Gene Ontology (GO)

11
  • GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0009379 A DNA helicase complex found at Holliday junctions where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • 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:0009378 Unwinding a DNA helix of DNA containing four-way junctions, including Holliday junctions, driven by ATP hydrolysis.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0048476 An endodeoxyribonuclease complex that resolves the 4-way DNA intermediates of a Holliday junction into two separate duplex DNA molecules. Can be branch-migration associated.
  • GO:0000400 Binding to a DNA segment containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
156 203 Gene3D G3DSA:1.10.8.10 -
159 201 Pfam PF07499 RuvA, C-terminal domain
159 201 InterPro IPR011114 Holliday junction DNA helicase RuvA, C-terminal
66 137 SUPERFAMILY SSF47781 RuvA domain 2-like
66 137 InterPro IPR010994 RuvA domain 2-like
108 127 SMART SM00278 HhH1_4
108 127 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
73 92 SMART SM00278 HhH1_4
73 92 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
1 66 Gene3D G3DSA:2.40.50.140 -
1 66 InterPro IPR012340 Nucleic acid-binding, OB-fold
67 142 Gene3D G3DSA:1.10.150.20 -
72 130 Pfam PF14520 Helix-hairpin-helix domain
1 203 Hamap MF_00031 Holliday junction branch migration complex subunit RuvA [ruvA].
1 203 InterPro IPR000085 Holliday junction branch migration complex subunit RuvA
158 200 CDD cd14332 UBA_RuvA_C
158 200 InterPro IPR011114 Holliday junction DNA helicase RuvA, C-terminal
1 62 Pfam PF01330 RuvA N terminal domain
1 62 InterPro IPR013849 DNA helicase, Holliday junction RuvA type, domain I, bacterial
67 142 FunFam G3DSA:1.10.150.20:FF:000012 Holliday junction ATP-dependent DNA helicase RuvA
1 203 NCBIfam TIGR00084 Holliday junction branch migration protein RuvA
156 203 FunFam G3DSA:1.10.8.10:FF:000008 Holliday junction ATP-dependent DNA helicase RuvA
1 65 FunFam G3DSA:2.40.50.140:FF:000083 Holliday junction ATP-dependent DNA helicase RuvA
157 201 SUPERFAMILY SSF46929 DNA helicase RuvA subunit, C-terminal domain
157 201 InterPro IPR036267 RuvA, C-terminal domain superfamily
1 63 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
1 63 InterPro IPR012340 Nucleic acid-binding, OB-fold

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_A0A0H3GQ62
AlphaFold — — full sequence — Viewing
ColabFold KP13_01621
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 0.218
2 0.007
3 0.004
4 0.003

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 1.91 0.032
2 1.17 0.009