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41  structures 2180  species 0  interactions 3078  sequences 35  architectures

Family: Endonuclease_5 (PF04493)

Summary: Endonuclease V

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This is the Wikipedia entry entitled "Endonuclease V". More...

Endonuclease V Edit Wikipedia article

Endonuclease V
2W36 ACD.png
Crystallographic structure of Thermotoga maritima endoV (blue) in complex with DNA (green and orange). The deamidated base is shown in yellow.[1]
Identifiers
SymbolENDOV
PfamPF04493
InterProIPR007581

Endonuclease V (endoV) is a highly conserved endonuclease enzyme family. The primary function of endoV differs significantly in prokaryotes and eukaryotes, as suggested by studies on the E. coli and human orthologs.

In prokaryotes endoV is primarily a deoxyribonuclease involved in DNA repair of deoxyinosine introduced into the genome by deamidation of adenine bases (EC 3.1.21.7).[2] However, it has broad substrate specificity and can also act on other types of DNA lesions[2] as well as on inosine-containing RNA.[3]

In eukaryotes endoV is primarily a ribonuclease and cleaves single-stranded RNA at the 3' position relative to an inosine base, which may be present due to RNA editing by deaminase enzymes (EC 3.1.26.-).[4] The human endoV localizes to the cytoplasm and nucleoli, suggesting a possible role in processes involving ribosomal RNA.[3] The human gene symbol is ENDOV.

References

  1. ^ Dalhus B, Arvai AS, Rosnes I, Olsen ØE, Backe PH, Alseth I, Gao H, Cao W, Tainer JA, Bjørås M (February 2009). "Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair". Nature Structural & Molecular Biology. 16 (2): 138–43. doi:10.1038/nsmb.1538. PMC 3560532. PMID 19136958.
  2. ^ a b Vik ES, Nawaz MS, Strøm Andersen P, Fladeby C, Bjørås M, Dalhus B, Alseth I (2013). "Endonuclease V cleaves at inosines in RNA". Nature Communications. 4: 2271. Bibcode:2013NatCo...4.2271S. doi:10.1038/ncomms3271. PMC 3741635. PMID 23912683.
  3. ^ a b Fladeby C, Vik ES, Laerdahl JK, Gran Neurauter C, Heggelund JE, Thorgaard E, Strøm-Andersen P, Bjørås M, Dalhus B, Alseth I (2012). "The human homolog of Escherichia coli endonuclease V is a nucleolar protein with affinity for branched DNA structures". PLOS ONE. 7 (11): e47466. Bibcode:2012PLoSO...747466F. doi:10.1371/journal.pone.0047466. PMC 3489907. PMID 23139746.
  4. ^ Morita Y, Shibutani T, Nakanishi N, Nishikura K, Iwai S, Kuraoka I (2013). "Human endonuclease V is a ribonuclease specific for inosine-containing RNA". Nature Communications. 4: 2273. Bibcode:2013NatCo...4.2273M. doi:10.1038/ncomms3273. PMC 3741642. PMID 23912718.


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Endonuclease V Provide feedback

Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents [1].

Literature references

  1. Guo G, Ding Y, Weiss B; , J Bacteriol 1997;179:310-316.: nfi, the gene for endonuclease V in Escherichia coli K-12. PUBMED:8990280 EPMC:8990280

  2. Demple B, Gates FT 3rd, Linn S; , Methods Enzymol 1980;65:224-231.: Purification and properties of Escherichia coli endodeoxyribonuclease V. PUBMED:6246346 EPMC:6246346


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007581

Endonuclease V is specific for single-stranded DNA, for duplex DNA that contains uracil, or that is damaged [ PUBMED:8990280 ]. Matrix metalloproteinase-1 (MMP-1) is the major enzyme responsible for collagen 1 digestion. It is induced by exposure to sunlight, but is reduced with treatment of DNA repair enzyme endonuclease V [ PUBMED:18459971 ]. This family consequently has potential medical importance [ PUBMED:18328204 ].

This endonuclease also appears in bifunctional enzymes, such as the bifunctional methyltransferase/endonuclease in Thermoplasma acidophilum.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(141)
Full
(3078)
Representative proteomes UniProt
(11770)
RP15
(515)
RP35
(1364)
RP55
(2862)
RP75
(4801)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(141)
Full
(3078)
Representative proteomes UniProt
(11770)
RP15
(515)
RP35
(1364)
RP55
(2862)
RP75
(4801)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(141)
Full
(3078)
Representative proteomes UniProt
(11770)
RP15
(515)
RP35
(1364)
RP55
(2862)
RP75
(4801)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Wood V
Previous IDs: Endonuc_V;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Wood V
Number in seed: 141
Number in full: 3078
Average length of the domain: 182.10 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 74.30 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.4 23.4
Trusted cut-off 23.5 23.4
Noise cut-off 23.3 23.2
Model length: 197
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Endonuclease_5 domain has been found. There are 41 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2K5U3 View 3D Structure Click here
A0A1D6LQ56 View 3D Structure Click here
A0A1D6LQ71 View 3D Structure Click here
A0B8N3 View 3D Structure Click here
A1RY04 View 3D Structure Click here
A4IDK7 View 3D Structure Click here
A5GD74 View 3D Structure Click here
A5UWX7 View 3D Structure Click here
A6TGQ5 View 3D Structure Click here
A8A9B8 View 3D Structure Click here
A8AKS5 View 3D Structure Click here
A9MHD1 View 3D Structure Click here
B2IWL4 View 3D Structure Click here
B2VG82 View 3D Structure Click here
B4EYT7 View 3D Structure Click here
B6IUZ1 View 3D Structure Click here
B7K379 View 3D Structure Click here
B8D509 View 3D Structure Click here
B8DZX0 View 3D Structure Click here
C5CGG9 View 3D Structure Click here
I1M9P5 View 3D Structure Click here
O30108 View 3D Structure Click here
O66824 View 3D Structure Click here
P52887 View 3D Structure Click here
P68738 View 3D Structure Click here
P68739 View 3D Structure Click here
P68741 View 3D Structure Click here
P96724 View 3D Structure Click here
Q0A5M1 View 3D Structure Click here
Q10348 View 3D Structure Click here
Q1DC68 View 3D Structure Click here
Q32AH1 View 3D Structure Click here
Q3IT64 View 3D Structure Click here
Q4E4E2 View 3D Structure Click here
Q4JB89 View 3D Structure Click here
Q556Q1 View 3D Structure Click here
Q5JI47 View 3D Structure Click here
Q5SIM2 View 3D Structure Click here
Q5V474 View 3D Structure Click here
Q5YQW3 View 3D Structure Click here