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Protein

Endonuclease 4

Gene

nfo

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin.

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.

Cofactori

Zn2+, Mn2+Note: Binds 3 Zn2+ ions. Can also bind Mn2+ ions.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi69Zinc 11
Metal bindingi109Zinc 11
Metal bindingi145Zinc 11
Metal bindingi145Zinc 21
Metal bindingi179Zinc 21
Metal bindingi182Zinc 31
Metal bindingi216Zinc 21
Metal bindingi229Zinc 31
Metal bindingi231Zinc 31
Metal bindingi261Zinc 21

GO - Molecular functioni

GO - Biological processi

  • base-excision repair Source: GO_Central
  • non-recombinational repair Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Manganese, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10651-MONOMER.
ECOL316407:JW2146-MONOMER.
MetaCyc:EG10651-MONOMER.
BRENDAi3.1.21.2. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease 4 (EC:3.1.21.2)
Alternative name(s):
Endodeoxyribonuclease IV
Endonuclease IV
Gene namesi
Name:nfo
Ordered Locus Names:b2159, JW2146
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10651. nfo.

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1293285.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001908381 – 285Endonuclease 4Add BLAST285

Proteomic databases

PaxDbiP0A6C1.
PRIDEiP0A6C1.

Expressioni

Inductioni

Endonuclease IV is induced by agents which generate superoxide radical anions.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

BioGridi4261799. 22 interactors.
DIPiDIP-47966N.
IntActiP0A6C1. 10 interactors.
MINTiMINT-1242700.
STRINGi511145.b2159.

Structurei

Secondary structure

1285
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 7Combined sources5
Helixi14 – 23Combined sources10
Beta strandi27 – 30Combined sources4
Beta strandi32 – 34Combined sources3
Helixi46 – 58Combined sources13
Helixi63 – 65Combined sources3
Beta strandi66 – 69Combined sources4
Helixi81 – 100Combined sources20
Beta strandi105 – 108Combined sources4
Turni114 – 116Combined sources3
Helixi119 – 136Combined sources18
Beta strandi141 – 145Combined sources5
Helixi158 – 167Combined sources10
Helixi171 – 173Combined sources3
Beta strandi174 – 179Combined sources6
Helixi180 – 186Combined sources7
Helixi193 – 206Combined sources14
Helixi209 – 211Combined sources3
Beta strandi212 – 217Combined sources6
Beta strandi219 – 222Combined sources4
Turni234 – 236Combined sources3
Beta strandi237 – 239Combined sources3
Helixi242 – 248Combined sources7
Helixi251 – 253Combined sources3
Beta strandi256 – 260Combined sources5
Helixi265 – 267Combined sources3
Helixi268 – 278Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QTWX-ray1.02A1-285[»]
1QUMX-ray1.55A1-285[»]
2NQ9X-ray1.45A1-285[»]
2NQHX-ray1.10A1-285[»]
2NQJX-ray2.45A/B1-285[»]
4K1GX-ray1.90A/B1-285[»]
ProteinModelPortaliP0A6C1.
SMRiP0A6C1.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A6C1.

Family & Domainsi

Sequence similaritiesi

Belongs to the AP endonuclease 2 family.Curated

Phylogenomic databases

eggNOGiENOG4105EFU. Bacteria.
COG0648. LUCA.
HOGENOMiHOG000224893.
InParanoidiP0A6C1.
KOiK01151.
OMAiMKYVGAH.
PhylomeDBiP0A6C1.

Family and domain databases

Gene3Di3.20.20.150. 1 hit.
HAMAPiMF_00152. Nfo. 1 hit.
InterProiIPR001719. AP_endonuc_2.
IPR018246. AP_endonuc_F2_Zn_BS.
IPR013022. Xyl_isomerase-like_TIM-brl.
[Graphical view]
PANTHERiPTHR21445. PTHR21445. 1 hit.
PfamiPF01261. AP_endonuc_2. 1 hit.
[Graphical view]
SMARTiSM00518. AP2Ec. 1 hit.
[Graphical view]
SUPFAMiSSF51658. SSF51658. 1 hit.
TIGRFAMsiTIGR00587. nfo. 1 hit.
PROSITEiPS00729. AP_NUCLEASE_F2_1. 1 hit.
PS00730. AP_NUCLEASE_F2_2. 1 hit.
PS00731. AP_NUCLEASE_F2_3. 1 hit.
PS51432. AP_NUCLEASE_F2_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A6C1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKYIGAHVSA AGGLANAAIR AAEIDATAFA LFTKNQRQWR AAPLTTQTID
60 70 80 90 100
EFKAACEKYH YTSAQILPHD SYLINLGHPV TEALEKSRDA FIDEMQRCEQ
110 120 130 140 150
LGLSLLNFHP GSHLMQISEE DCLARIAESI NIALDKTQGV TAVIENTAGQ
160 170 180 190 200
GSNLGFKFEH LAAIIDGVED KSRVGVCIDT CHAFAAGYDL RTPAECEKTF
210 220 230 240 250
ADFARTVGFK YLRGMHLNDA KSTFGSRVDR HHSLGEGNIG HDAFRWIMQD
260 270 280
DRFDGIPLIL ETINPDIWAE EIAWLKAQQT EKAVA
Length:285
Mass (Da):31,480
Last modified:June 7, 2005 - v1
Checksum:iEAAE5861E54C47FD
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti10A → R in AAA24216 (PubMed:2460435).Curated1
Sequence conflicti273A → T in AAA60529 (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M22591 Genomic DNA. Translation: AAA24216.1.
U00007 Genomic DNA. Translation: AAA60529.1.
U00096 Genomic DNA. Translation: AAC75220.1.
AP009048 Genomic DNA. Translation: BAE76636.1.
PIRiF64984. NDEC4.
RefSeqiNP_416664.1. NC_000913.3.
WP_000873894.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75220; AAC75220; b2159.
BAE76636; BAE76636; BAE76636.
GeneIDi946669.
KEGGiecj:JW2146.
eco:b2159.
PATRICi32119667. VBIEscCol129921_2244.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M22591 Genomic DNA. Translation: AAA24216.1.
U00007 Genomic DNA. Translation: AAA60529.1.
U00096 Genomic DNA. Translation: AAC75220.1.
AP009048 Genomic DNA. Translation: BAE76636.1.
PIRiF64984. NDEC4.
RefSeqiNP_416664.1. NC_000913.3.
WP_000873894.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QTWX-ray1.02A1-285[»]
1QUMX-ray1.55A1-285[»]
2NQ9X-ray1.45A1-285[»]
2NQHX-ray1.10A1-285[»]
2NQJX-ray2.45A/B1-285[»]
4K1GX-ray1.90A/B1-285[»]
ProteinModelPortaliP0A6C1.
SMRiP0A6C1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261799. 22 interactors.
DIPiDIP-47966N.
IntActiP0A6C1. 10 interactors.
MINTiMINT-1242700.
STRINGi511145.b2159.

Chemistry databases

ChEMBLiCHEMBL1293285.

Proteomic databases

PaxDbiP0A6C1.
PRIDEiP0A6C1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75220; AAC75220; b2159.
BAE76636; BAE76636; BAE76636.
GeneIDi946669.
KEGGiecj:JW2146.
eco:b2159.
PATRICi32119667. VBIEscCol129921_2244.

Organism-specific databases

EchoBASEiEB0645.
EcoGeneiEG10651. nfo.

Phylogenomic databases

eggNOGiENOG4105EFU. Bacteria.
COG0648. LUCA.
HOGENOMiHOG000224893.
InParanoidiP0A6C1.
KOiK01151.
OMAiMKYVGAH.
PhylomeDBiP0A6C1.

Enzyme and pathway databases

BioCyciEcoCyc:EG10651-MONOMER.
ECOL316407:JW2146-MONOMER.
MetaCyc:EG10651-MONOMER.
BRENDAi3.1.21.2. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A6C1.
PROiP0A6C1.

Family and domain databases

Gene3Di3.20.20.150. 1 hit.
HAMAPiMF_00152. Nfo. 1 hit.
InterProiIPR001719. AP_endonuc_2.
IPR018246. AP_endonuc_F2_Zn_BS.
IPR013022. Xyl_isomerase-like_TIM-brl.
[Graphical view]
PANTHERiPTHR21445. PTHR21445. 1 hit.
PfamiPF01261. AP_endonuc_2. 1 hit.
[Graphical view]
SMARTiSM00518. AP2Ec. 1 hit.
[Graphical view]
SUPFAMiSSF51658. SSF51658. 1 hit.
TIGRFAMsiTIGR00587. nfo. 1 hit.
PROSITEiPS00729. AP_NUCLEASE_F2_1. 1 hit.
PS00730. AP_NUCLEASE_F2_2. 1 hit.
PS00731. AP_NUCLEASE_F2_3. 1 hit.
PS51432. AP_NUCLEASE_F2_4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiEND4_ECOLI
AccessioniPrimary (citable) accession number: P0A6C1
Secondary accession number(s): P12638, P78086, Q2MAS0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: November 2, 2016
This is version 107 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.