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Protein

Endonuclease V

Gene

nfi

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. In vitro, can also cleave single-stranded substrates with inosine, double-stranded DNA with apurinic sites, or DNA sites with uracil or a mismatched base. When present in molar excess, two protein molecules can bind to the same DNA substrate and effect cleavage of both strands (in vitro).UniRule annotation1 Publication

Catalytic activityi

Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi43Magnesium1
Metal bindingi110Magnesium1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BRENDAi3.1.21.7. 6331.

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease VUniRule annotation (EC:3.1.21.7UniRule annotation)
Alternative name(s):
Deoxyinosine 3'endonucleaseUniRule annotation
Deoxyribonuclease VUniRule annotation
Short name:
DNase VUniRule annotation
Gene namesi
Name:nfiUniRule annotation
Ordered Locus Names:TM_1865
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi43D → A: Complete loss of enzyme activity. 1 Publication1
Mutagenesisi80Y → A: Reduced affinity for DNA. No effect on cleavage of DNA containing inosine. Abolishes cleavage at apurinic sites. 1 Publication1
Mutagenesisi88R → A: Reduced affinity for DNA. No effect on cleavage of DNA containing inosine. Abolishes cleavage at apurinic sites. 1 Publication1
Mutagenesisi89E → A: Strongly reduced cleavage of DNA containing inosine. 1 Publication1
Mutagenesisi105D → A: No effect on cleavage of DNA containing inosine. 1
Mutagenesisi110D → A: Complete loss of enzyme activity. 1 Publication1
Mutagenesisi116H → A: Reduced affinity for DNA. No effect on cleavage of DNA containing inosine. Abolishes cleavage at apurinic sites. 1 Publication1
Mutagenesisi125H → A: No effect on cleavage of DNA containing inosine. 1 Publication1
Mutagenesisi139K → A: No effect on DNA binding. No effect on cleavage of DNA containing inosine. Strongly reduced cleavage at apurinic sites. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001596741 – 225Endonuclease VAdd BLAST225

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei80Interaction with target DNA1

Protein-protein interaction databases

DIPiDIP-48482N.
STRINGi243274.TM1865.

Structurei

Secondary structure

1225
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi13 – 23Combined sources11
Helixi24 – 26Combined sources3
Beta strandi37 – 48Combined sources12
Beta strandi51 – 60Combined sources10
Turni61 – 64Combined sources4
Beta strandi65 – 75Combined sources11
Helixi86 – 97Combined sources12
Beta strandi105 – 111Combined sources7
Beta strandi113 – 116Combined sources4
Helixi122 – 130Combined sources9
Beta strandi134 – 140Combined sources7
Beta strandi143 – 145Combined sources3
Beta strandi151 – 154Combined sources4
Beta strandi156 – 161Combined sources6
Beta strandi164 – 170Combined sources7
Beta strandi179 – 183Combined sources5
Helixi189 – 199Combined sources11
Helixi208 – 220Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2W35X-ray2.15A/B1-225[»]
2W36X-ray2.10A/B1-225[»]
3HD0X-ray2.70A/B/D1-222[»]
4B20X-ray2.75A/B1-225[»]
SMRiQ9X2H9.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9X2H9.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni139 – 141Interaction with target DNA3
Regioni214 – 221Interaction with target DNA8

Sequence similaritiesi

Belongs to the endonuclease V family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105Y7X. Bacteria.
COG1515. LUCA.
InParanoidiQ9X2H9.
KOiK05982.
OMAiREYPALM.

Family and domain databases

CDDicd06559. Endonuclease_V. 1 hit.
HAMAPiMF_00801. Endonuclease_5. 1 hit.
InterProiIPR007581. Endonuclease-V.
[Graphical view]
PfamiPF04493. Endonuclease_5. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9X2H9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDYRQLHRWD LPPEEAIKVQ NELRKKIKLT PYEGEPEYVA GVDLSFPGKE
60 70 80 90 100
EGLAVIVVLE YPSFKILEVV SERGEITFPY IPGLLAFREG PLFLKAWEKL
110 120 130 140 150
RTKPDVVVFD GQGLAHPRKL GIASHMGLFI EIPTIGVAKS RLYGTFKMPE
160 170 180 190 200
DKRCSWSYLY DGEEIIGCVI RTKEGSAPIF VSPGHLMDVE SSKRLIKAFT
210 220
LPGRRIPEPT RLAHIYTQRL KKGLF
Length:225
Mass (Da):25,598
Last modified:November 1, 1999 - v1
Checksum:i84250E645E410445
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36927.1.
PIRiB72202.
RefSeqiNP_229661.1. NC_000853.1.
WP_004082416.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD36927; AAD36927; TM_1865.
GeneIDi897801.
KEGGitma:TM1865.
PATRICi23938719. VBITheMar51294_1886.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36927.1.
PIRiB72202.
RefSeqiNP_229661.1. NC_000853.1.
WP_004082416.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2W35X-ray2.15A/B1-225[»]
2W36X-ray2.10A/B1-225[»]
3HD0X-ray2.70A/B/D1-222[»]
4B20X-ray2.75A/B1-225[»]
SMRiQ9X2H9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48482N.
STRINGi243274.TM1865.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36927; AAD36927; TM_1865.
GeneIDi897801.
KEGGitma:TM1865.
PATRICi23938719. VBITheMar51294_1886.

Phylogenomic databases

eggNOGiENOG4105Y7X. Bacteria.
COG1515. LUCA.
InParanoidiQ9X2H9.
KOiK05982.
OMAiREYPALM.

Enzyme and pathway databases

BRENDAi3.1.21.7. 6331.

Miscellaneous databases

EvolutionaryTraceiQ9X2H9.

Family and domain databases

CDDicd06559. Endonuclease_V. 1 hit.
HAMAPiMF_00801. Endonuclease_5. 1 hit.
InterProiIPR007581. Endonuclease-V.
[Graphical view]
PfamiPF04493. Endonuclease_5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNFI_THEMA
AccessioniPrimary (citable) accession number: Q9X2H9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 7, 2004
Last sequence update: November 1, 1999
Last modified: November 2, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.