Protein profile

KP13_03032

UvrABC system protein B

Genome: KpKP13

Gene: uvrB AHE45582.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GKA2
Amino acids 673
Annotations 11
Features 46
PDB binders 6
Druggability 0.333

Overview

Basic information about this protein and its source genome.

Accession
KP13_03032
Gene
uvrB AHE45582.1
Status
annotated
Amino acids
673
Structure source
AlphaFold + ColabFold
GO
GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0006289 A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts). GO:0005515 Binding to a protein. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0009380 Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
33.036
Human E-value
6.44e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
79.315
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
87.49

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 0.333
Structure A0A0H3GKA2
Pocket Pocket 43
P2Rank 0.91
Structure A0A0H3GKA2
Pocket Pocket 1
ColabFold model
FPocket 0.257 · Pocket 19
P2Rank 0.877 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 4106 / 4744 genomes with a hit
Normalized 0.866

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:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0006289 A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
  • GO:0005515 Binding to a protein.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0009380 Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009381 Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
  • GO:0004386 Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

46 records
Show feature table
Start End DB Term Name
231 414 FunFam G3DSA:3.40.50.300:FF:000477 UvrABC system protein B
636 656 Coils Coil Coil
5 415 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
5 415 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
37 584 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
37 584 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
264 284 Coils Coil Coil
4 243 Gene3D G3DSA:3.40.50.300 -
4 243 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
269 414 Gene3D G3DSA:3.40.50.300 -
269 414 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
431 597 ProSiteProfiles PS51194 Superfamilies 1 and 2 helicase C-terminal domain profile.
431 597 InterPro IPR001650 Helicase, C-terminal
5 666 NCBIfam TIGR00631 excinuclease ABC subunit UvrB
5 666 InterPro IPR004807 UvrABC system, subunit B
26 183 ProSiteProfiles PS51192 Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
26 183 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
9 425 SMART SM00487 ultradead3
9 425 InterPro IPR014001 Helicase superfamily 1/2, ATP-binding domain
634 667 Pfam PF02151 UvrB/uvrC motif
634 667 InterPro IPR001943 UVR domain
3 668 Hamap MF_00204 UvrABC system protein B [uvrB].
3 668 InterPro IPR004807 UvrABC system, subunit B
441 544 Pfam PF00271 Helicase conserved C-terminal domain
441 544 InterPro IPR001650 Helicase, C-terminal
633 668 ProSiteProfiles PS50151 UVR domain profile.
633 668 InterPro IPR001943 UVR domain
613 673 Gene3D G3DSA:4.10.860.10 UVR domain
625 669 SUPERFAMILY SSF46600 C-terminal UvrC-binding domain of UvrB
625 669 InterPro IPR036876 UVR domain superfamily
159 249 Pfam PF17757 UvrB interaction domain
159 249 InterPro IPR041471 UvrB, interaction domain
3 669 PANTHER PTHR24029 UVRABC SYSTEM PROTEIN B
3 669 InterPro IPR004807 UvrABC system, subunit B
415 590 FunFam G3DSA:3.40.50.300:FF:000257 UvrABC system protein B
552 593 Pfam PF12344 Ultra-violet resistance protein B
552 593 InterPro IPR024759 UvrB, YAD/RRR-motif-containing domain
460 546 SMART SM00490 helicmild6
460 546 InterPro IPR001650 Helicase, C-terminal
16 92 Pfam PF04851 Type III restriction enzyme, res subunit
16 92 InterPro IPR006935 Helicase/UvrB, N-terminal
415 590 Gene3D G3DSA:3.40.50.300 -
415 590 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
5 414 CDD cd17916 DEXHc_UvrB
1 230 FunFam G3DSA:3.40.50.300:FF:000401 UvrABC system protein B
420 590 CDD cd18790 SF2_C_UvrB

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_A0A0H3GKA2
AlphaFold full sequence Viewing
ColabFold KP13_03032
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
43 0.333

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 21.99 0.876
2 10.06 0.542
3 4.67 0.203
4 2.38 0.063
5 1.72 0.03

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

56 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
ANP Q9NR30 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BEF P20449 66.0 Da LogP 0.88 TPSA 0.0 ✓ Ro5 ✓ Clean [Be-](F)(F)F
FLQ P56981 516.6 Da LogP 4.09 TPSA 134.2 1 viol. ✓ Clean CC(=O)NCCCCCCNC(=O)c1ccc2c(c1)C3(c4ccc(cc4Oc5c3…
FLU P37954 332.3 Da LogP 3.97 TPSA 87.7 ✓ Ro5 ✓ Clean c1ccc(c(c1)C2=C3C=CC(=O)C=C3Oc4c2ccc(c4)O)C(=O)O
IHP P20449 660.0 Da LogP -3.13 TPSA 400.6 3 viol. ✓ Clean C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O…
M2A P20449 560.4 Da LogP 0.16 TPSA 250.7 3 viol. ✓ Clean CNc1ccccc1C(=O)O[C@@H]2[C@@H]([C@@H](O[C@H]2n3c…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.