Protein profile

PA3738

site-specific tyrosine recombinase XerD

Genome: NC_002516.2

Gene: PA3738 xerD Structure source: AlphaFold UniProt Q9HXQ6
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Amino acids 298
Annotations 11
Features 22
PDB binders 0
Druggability 0.859

Overview

Basic information about this protein and its source genome.

Accession
PA3738
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3738 xerD
Status
annotated
Amino acids
298
Structure source
AlphaFold
GO
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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0009037 Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site. GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.859
Structure –
Pocket –

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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0009037 Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
  • 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:0006313 A type of transposition in which a transposable element (transposon) is moved to another part of a genome, either by a cut-and-paste mechanism or a replicative mechanism.
  • GO:0071139 The cleavage and rejoining of intermediates, such as Holliday junctions, formed during DNA recombination to produce two intact molecules in which genetic material has been exchanged.
  • GO:0015074 The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome.
  • GO:0009009 Catalysis of the formation of new phosphodiester bonds between a pair of short, unique target DNA sequences.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
5 298 Hamap MF_01807 Tyrosine recombinase XerD [xerD].
5 298 InterPro IPR011932 Tyrosine recombinase XerD
6 99 Gene3D G3DSA:1.10.150.130 -
6 99 InterPro IPR010998 Integrase/recombinase, N-terminal
113 283 Pfam PF00589 Phage integrase family
113 283 InterPro IPR002104 Integrase, catalytic domain
11 297 NCBIfam TIGR02225 site-specific tyrosine recombinase XerD
11 297 InterPro IPR011932 Tyrosine recombinase XerD
8 288 SUPERFAMILY SSF56349 DNA breaking-rejoining enzymes
8 288 InterPro IPR011010 DNA breaking-rejoining enzyme, catalytic core
109 292 ProSiteProfiles PS51898 Tyrosine recombinase domain profile.
109 292 InterPro IPR002104 Integrase, catalytic domain
49 282 PANTHER PTHR30629 PROPHAGE INTEGRASE
7 298 Hamap MF_01808 Tyrosine recombinase XerC [xerC].
7 298 InterPro IPR023009 Tyrosine recombinase XerC/XerD
3 88 ProSiteProfiles PS51900 Core-binding (CB) domain profile.
3 88 InterPro IPR044068 Core-binding (CB) domain
116 287 CDD cd00798 INT_XerDC_C
112 292 Gene3D G3DSA:1.10.443.10 Intergrase catalytic core
112 292 InterPro IPR013762 Integrase-like, catalytic domain superfamily
9 90 Pfam PF02899 Phage integrase, N-terminal SAM-like domain
9 90 InterPro IPR004107 Integrase, SAM-like, N-terminal

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

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Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3738
AlphaFold — — full sequence — Viewing
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 0.859