Q87SC6 (END4_VIBPA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Probable endonuclease 4
EC=3.1.21.2

Alternative name(s):
Endodeoxyribonuclease IV
Endonuclease IV

Gene names

Name:	nfo
Ordered Locus Names:	VP0498

Organism

Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) [Complete proteome] [HAMAP]

Taxonomic identifier

223926 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio › Vibrio harveyi group › Vibrio parahaemolyticus

Protein attributes

Sequence length	295 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	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 By similarity. HAMAP-Rule MF_00152
Catalytic activity	Endonucleolytic cleavage to 5'-phosphooligonucleotide end-products. HAMAP-Rule MF_00152
Cofactor	Binds 3 zinc ions By similarity.
Sequence similarities	Belongs to the AP endonuclease 2 family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Ligand	Metal-binding Zinc
Molecular function	Endonuclease Hydrolase Nuclease
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: HAMAP nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Cellular_component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro deoxyribonuclease IV (phage-T4-induced) activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 295	295	Probable endonuclease 4 HAMAP-Rule MF_00152		PRO_0000190885
Sites
	Metal binding	78	1	Zinc 1 By similarity
	Metal binding	118	1	Zinc 1 By similarity
	Metal binding	154	1	Zinc 1 By similarity
	Metal binding	154	1	Zinc 2 By similarity
	Metal binding	188	1	Zinc 2 By similarity
	Metal binding	191	1	Zinc 3 By similarity
	Metal binding	225	1	Zinc 2 By similarity
	Metal binding	238	1	Zinc 3 By similarity
	Metal binding	240	1	Zinc 3 By similarity
	Metal binding	270	1	Zinc 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q87SC6 [UniParc]. Last modified May 23, 2003. Version 1. Checksum: 784D0378858E3E0C	FASTA	295	33,017
	10 20 30 40 50 60 MTNMKNKFGN KLIGAHVSAA GGVDQAPLRA REIGANAFAL FTKNQRQWVA KPLEAKTISA 70 80 90 100 110 120 FKANCKMLGF GAEHILPHDS YLINLGAPEA EKLDKSRAAF IDEMERCNQL GLTLLNFHPG 130 140 150 160 170 180 SHLKKVSEQE CLATIAESIN LAHKTVPDVV AVIENTAGQG TNLGWKFEHL AEIIEQVEDK 190 200 210 220 230 240 DRVGVCIDTC HTFTAGYDLR TKEDCERTFA EFDRIVGMHY LRAMHLNDSK VEFASKVDRH 250 260 270 280 290 HSLGKGEIGW DCFEYIAKDS RFDGIPLILE TIDPDIWQQE INTLRQFHLA AINNQ

References

[1]

"Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae." Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T. Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: RIMD 2210633.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000031 Genomic DNA. Translation: BAC58761.1.
RefSeq	NP_796877.1. NC_004603.1.
3D structure databases
ProteinModelPortal	Q87SC6.
SMR	Q87SC6. Positions 11-285.
ModBase	Search...
Protein-protein interaction databases
STRING	223926.VP0498.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAC58761; BAC58761; BAC58761.
GeneID	1187966.
KEGG	vpa:VP0498.
PATRIC	20139202. VBIVibPar50997_0475.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0648.
HOGENOM	HOG000224893.
KO	K01151.
OMA	INLGHPD.
ProtClustDB	PRK01060.
Family and domain databases
Gene3D	3.20.20.150. 1 hit.
HAMAP	MF_00152. Nfo.
InterPro	IPR018246. AP_endonuc_F2_Zn_BS. IPR001719. Endodeoxyribonuclease_IV. IPR013022. Xyl_isomerase-like_TIM-brl. [Graphical view]
PANTHER	PTHR21445. PTHR21445. 1 hit.
Pfam	PF01261. AP_endonuc_2. 1 hit. [Graphical view]
SMART	SM00518. AP2Ec. 1 hit. [Graphical view]
SUPFAM	SSF51658. Xyl_isomerase-like_TIM-brl. 1 hit.
TIGRFAMs	TIGR00587. nfo. 1 hit.
PROSITE	PS00729. 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]
ProtoNet	Search...

Entry information

Entry name

END4_VIBPA

Accession

Primary (citable) accession number: Q87SC6

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 23, 2003
Last sequence update:	May 23, 2003
Last modified:	May 1, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program