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Protein

Probable endonuclease 4

Gene

nfo

Organism
Onion yellows phytoplasma (strain OY-M)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

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.UniRule annotation

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.UniRule annotation

Cofactori

Zn2+UniRule annotationNote: Binds 3 Zn2+ ions.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi71 – 711Zinc 1UniRule annotation
Metal bindingi111 – 1111Zinc 1UniRule annotation
Metal bindingi148 – 1481Zinc 1UniRule annotation
Metal bindingi148 – 1481Zinc 2UniRule annotation
Metal bindingi182 – 1821Zinc 2UniRule annotation
Metal bindingi185 – 1851Zinc 3UniRule annotation
Metal bindingi217 – 2171Zinc 2UniRule annotation
Metal bindingi230 – 2301Zinc 3UniRule annotation
Metal bindingi232 – 2321Zinc 3UniRule annotation
Metal bindingi262 – 2621Zinc 2UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciMORG262768:GHF5-466-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable endonuclease 4UniRule annotation (EC:3.1.21.2UniRule annotation)
Alternative name(s):
Endodeoxyribonuclease IVUniRule annotation
Endonuclease IVUniRule annotation
Gene namesi
Name:nfoUniRule annotation
Ordered Locus Names:PAM_454
OrganismiOnion yellows phytoplasma (strain OY-M)
Taxonomic identifieri262768 [NCBI]
Taxonomic lineageiBacteriaTenericutesMollicutesAcholeplasmatalesAcholeplasmataceaeCandidatus PhytoplasmaCandidatus Phytoplasma asteris
Proteomesi
  • UP000002523 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 292292Probable endonuclease 4PRO_0000190862Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi262768.PAM_454.

Structurei

3D structure databases

ProteinModelPortaliQ6YQC1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the AP endonuclease 2 family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105EFU. Bacteria.
COG0648. LUCA.
HOGENOMiHOG000224895.
KOiK01151.
OMAiIYLGAPQ.
OrthoDBiEOG6Z0QCM.

Family and domain databases

Gene3Di3.20.20.150. 1 hit.
HAMAPiMF_00152. Nfo.
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.

Q6YQC1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLFLGSHVAM KKPHNFQGAI QTAISYGANA LMVYSGAPQN TIRTKTEELK
60 70 80 90 100
IKQALEIVQN NNLSLNNLVG HAPYIINLAN PDETKRAFAI DFLSQELERF
110 120 130 140 150
AAMKINKMVL HPGNYLKTNP QEGISLIAQS LDLIFEKTKH LKTQVALETM
160 170 180 190 200
AGKGTEIGKN LEELQQIRTQ VKNNTRVSFC LDTCHLFDAG YDLKENLEEI
210 220 230 240 250
IQKIDSILGF QNISVIHIND SKNECNSHKD RHENIGFGKI GFETLLKIIY
260 270 280 290
HRAFACIPKI LETPYINDKA PYKREIEMIK AKAFNPELKK LF
Length:292
Mass (Da):33,082
Last modified:July 5, 2004 - v1
Checksum:i5BADAC30E2B8F833
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006628 Genomic DNA. Translation: BAD04539.1.
RefSeqiWP_011160805.1. NC_005303.2.

Genome annotation databases

EnsemblBacteriaiBAD04539; BAD04539; PAM_454.
KEGGipoy:PAM_454.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006628 Genomic DNA. Translation: BAD04539.1.
RefSeqiWP_011160805.1. NC_005303.2.

3D structure databases

ProteinModelPortaliQ6YQC1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi262768.PAM_454.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD04539; BAD04539; PAM_454.
KEGGipoy:PAM_454.

Phylogenomic databases

eggNOGiENOG4105EFU. Bacteria.
COG0648. LUCA.
HOGENOMiHOG000224895.
KOiK01151.
OMAiIYLGAPQ.
OrthoDBiEOG6Z0QCM.

Enzyme and pathway databases

BioCyciMORG262768:GHF5-466-MONOMER.

Family and domain databases

Gene3Di3.20.20.150. 1 hit.
HAMAPiMF_00152. Nfo.
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...

Publicationsi

  1. "Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma."
    Oshima K., Kakizawa S., Nishigawa H., Jung H.-Y., Wei W., Suzuki S., Arashida R., Nakata D., Miyata S., Ugaki M., Namba S.
    Nat. Genet. 36:27-29(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: OY-M.

Entry informationi

Entry nameiEND4_ONYPE
AccessioniPrimary (citable) accession number: Q6YQC1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: July 5, 2004
Last modified: November 11, 2015
This is version 79 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

Complete proteome, Reference proteome

Documents

  1. 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.