Q8IUX4 (ABC3F_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA dC->dU-editing enzyme APOBEC-3F
EC=3.5.4.-

Alternative name(s):
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F

Gene names

Name:

APOBEC3F

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	373 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Host cellular restriction factor that may have antiviral activities against exogenous and endogenous viruses, as well as retrotransposons. After being packaged into HIV-1 virions, blocks productive infection by massively editing dC residues to dU on the DNA minus strand during reverse transcription. The editing of the minus strand DNA of HIV-1 during reverse transcription leads to G-to-A transitions in the plus strand. The inhibition of viral replication is either due to the degradation of the minus strand before its integration or to the lethality of the hypermutations. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation. Ref.7 Ref.8 Ref.9 Ref.11
Catalytic activity	Cytidine + H2O = uridine + NH3.
Cofactor	Zinc By similarity.
Subunit structure	Forms heterodimers with APOBEC3G. Binds HIV-1 Vif. In the absence of Vif protein, specifically packaged into HIV-1 virions.
Subcellular location	Cytoplasm Ref.8.
Tissue specificity	Widely expressed. Highly expressed in ovary. Ref.5 Ref.7 Ref.10
Miscellaneous	It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.
Sequence similarities	Belongs to the cytidine and deoxycytidylate deaminase family.

Ontologies

Keywords
Biological process	Antiviral defense
Cellular component	Cytoplasm
Coding sequence diversity	Alternative splicing Polymorphism
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA demethylation Inferred from direct assay Ref.11. Source: UniProtKB base conversion or substitution editing Inferred from direct assay. Source: HGNC innate immune response Inferred from direct assay. Source: HGNC negative regulation of retroviral genome replication Inferred from direct assay. Source: HGNC negative regulation of transposition Inferred from direct assay Ref.8Ref.9. Source: UniProtKB positive regulation of defense response to virus by host Inferred from direct assay. Source: HGNC response to virus Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	apolipoprotein B mRNA editing enzyme complex Traceable author statement. Source: HGNC cytoplasm Inferred from direct assay Ref.8. Source: UniProtKB
Molecular function	RNA binding Inferred from direct assay Ref.5. Source: HGNC cytidine deaminase activity Inferred from direct assay. Source: HGNC zinc ion binding Inferred from direct assay Ref.5. Source: HGNC
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q8IUX4-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q8IUX4-2)

The sequence of this isoform differs from the canonical sequence as follows:
     58-79: VYSQPEHHAEMCFLSWFCGNQL → VPPGLQSLCRQELSQLGKQTTH
     80-373: Missing.

Note: May be due to a competing donor splice site. No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 373	373	DNA dC->dU-editing enzyme APOBEC-3F		PRO_0000171757
Sites
	Active site	251	1	Proton donor By similarity
	Metal binding	65	1	Zinc By similarity
	Metal binding	96	1	Zinc By similarity
	Metal binding	99	1	Zinc By similarity
Natural variations
	Alternative sequence	58 – 79	22	VYSQP…CGNQL → VPPGLQSLCRQELSQLGKQT TH in isoform 2.		VSP_009803
	Alternative sequence	80 – 373	294	Missing in isoform 2.		VSP_009804
	Natural variant	48	1	R → P. Ref.4 Corresponds to variant rs35053197 [ dbSNP | Ensembl ].		VAR_038355
	Natural variant	61	1	Q → L. Corresponds to variant rs2076109 [ dbSNP | Ensembl ].		VAR_018145
	Natural variant	97	1	P → L. Corresponds to variant rs2076110 [ dbSNP | Ensembl ].		VAR_018146
	Natural variant	108	1	A → S. Ref.4 Corresponds to variant rs2020390 [ dbSNP | Ensembl ].		VAR_018147
	Natural variant	178	1	A → T. Ref.1 Corresponds to variant rs34182094 [ dbSNP | Ensembl ].		VAR_025058
	Natural variant	231	1	V → I. Ref.1 Corresponds to variant rs2076101 [ dbSNP | Ensembl ].		VAR_018148
	Natural variant	307	1	Y → C. Ref.1 Corresponds to variant rs12157816 [ dbSNP | Ensembl ].		VAR_025059

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 23, 2007. Version 3. Checksum: AF1A0E13830695F4	FASTA	373	45,020
	10 20 30 40 50 60 MKPHFRNTVE RMYRDTFSYN FYNRPILSRR NTVWLCYEVK TKGPSRPRLD AKIFRGQVYS 70 80 90 100 110 120 QPEHHAEMCF LSWFCGNQLP AYKCFQITWF VSWTPCPDCV AKLAEFLAEH PNVTLTISAA 130 140 150 160 170 180 RLYYYWERDY RRALCRLSQA GARVKIMDDE EFAYCWENFV YSEGQPFMPW YKFDDNYAFL 190 200 210 220 230 240 HRTLKEILRN PMEAMYPHIF YFHFKNLRKA YGRNESWLCF TMEVVKHHSP VSWKRGVFRN 250 260 270 280 290 300 QVDPETHCHA ERCFLSWFCD DILSPNTNYE VTWYTSWSPC PECAGEVAEF LARHSNVNLT 310 320 330 340 350 360 IFTARLYYFW DTDYQEGLRS LSQEGASVEI MGYKDFKYCW ENFVYNDDEP FKPWKGLKYN 370 FLFLDSKLQE ILE
	Isoform 2 [UniParc]. Checksum: 03ABEACA44AB0748	FASTA	79	9,445
	10 20 30 40 50 60 MKPHFRNTVE RMYRDTFSYN FYNRPILSRR NTVWLCYEVK TKGPSRPRLD AKIFRGQVPP 70 GLQSLCRQEL SQLGKQTTH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	SeattleSNPs variation discovery resource Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS THR-178; ILE-231 AND CYS-307.
[2]	"The DNA sequence of human chromosome 22." Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M. , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L., Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L., Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N., Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R., Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y., Wright H. Nature 402:489-495(1999) [PubMed: 10591208] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANTS PRO-48 AND SER-108. Tissue: Pancreas, Spleen and Uterus.
[5]	"An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22." Jarmuz A., Chester A., Bayliss J., Gisbourne J., Dunham I., Scott J., Navaratnam N. Genomics 79:285-296(2002) [PubMed: 11863358] [Abstract] Cited for: GENE FAMILY ORGANIZATION, TISSUE SPECIFICITY.
[6]	"Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business." Wedekind J.E., Dance G.S.C., Sowden M.P., Smith H.C. Trends Genet. 19:207-216(2003) [PubMed: 12683974] [Abstract] Cited for: REVIEW ON APOBEC FAMILIES.
[7]	"A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins." Wiegand H.L., Doehle B.P., Bogerd H.P., Cullen B.R. EMBO J. 23:2451-2458(2004) [PubMed: 15152192] [Abstract] Cited for: FUNCTION IN HIV-1 INFECTIVITY, TISSUE SPECIFICITY.
[8]	"APOBEC3A is a potent inhibitor of adeno-associated virus and retrotransposons." Chen H., Lilley C.E., Yu Q., Lee D.V., Chou J., Narvaiza I., Landau N.R., Weitzman M.D. Curr. Biol. 16:480-485(2006) [PubMed: 16527742] [Abstract] Cited for: FUNCTION IN RETROTRANSPOSITION, SUBCELLULAR LOCATION.
[9]	"APOBEC3 proteins mediate the clearance of foreign DNA from human cells." Stenglein M.D., Burns M.B., Li M., Lengyel J., Harris R.S. Nat. Struct. Mol. Biol. 17:222-229(2010) [PubMed: 20062055] [Abstract] Cited for: FUNCTION IN RETROTRANSPOSITION.
[10]	"Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction." Refsland E.W., Stenglein M.D., Shindo K., Albin J.S., Brown W.L., Harris R.S. Nucleic Acids Res. 38:4274-4284(2010) [PubMed: 20308164] [Abstract] Cited for: TISSUE SPECIFICITY.
[11]	"Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain." Guo J.U., Su Y., Zhong C., Ming G.L., Song H. Cell 145:423-434(2011) [PubMed: 21496894] [Abstract] Cited for: FUNCTION IN DNA DEMETHYLATION.
+	Additional computationally mapped references.

Web resources

SeattleSNPs

Cross-references

Sequence databases
EMBL GenBank DDBJ	DQ146365 Genomic DNA. Translation: AAZ38720.1. AL022318 Genomic DNA. Translation: CAQ09853.1. CH471095 Genomic DNA. Translation: EAW60289.1. BC038808 mRNA. Translation: AAH38808.1. BC061914 mRNA. Translation: AAH61914.1.
IPI	IPI00409765. IPI00477614.
RefSeq	NP_660341.2. NM_145298.5.
UniGene	Hs.659809. Hs.660143.
3D structure databases
ProteinModelPortal	Q8IUX4.
SMR	Q8IUX4. Positions 10-190, 193-373.
ModBase	Search...
Protein-protein interaction databases
STRING	Q8IUX4.
Polymorphism databases
DMDM	161784334.
Proteomic databases
PRIDE	Q8IUX4.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000308521; ENSP00000309749; ENSG00000128394.
GeneID	200316.
KEGG	hsa:200316.
NMPDR	fig|9606.3.peg.21730.
UCSC	uc003aww.1. human.
Organism-specific databases
CTD	200316.
GeneCards	GC22P039436.
HGNC	HGNC:17356. APOBEC3F.
MIM	608993. gene.
neXtProt	NX_Q8IUX4.
GenAtlas	Search...
Phylogenomic databases
GeneTree	ENSGT00530000062933.
HOVERGEN	HBG050434.
InParanoid	Q8IUX4.
OrthoDB	EOG480HX1.
Enzyme and pathway databases
BRENDA	3.5.4.5. 2681.
Gene expression databases
ArrayExpress	Q8IUX4.
Bgee	Q8IUX4.
CleanEx	HS_APOBEC3F.
Genevestigator	Q8IUX4.
GermOnline	ENSG00000128394. Homo sapiens.
Family and domain databases
InterPro	IPR016192. APOBEC/CMP_deaminase_Zn-bd. IPR007904. APOBEC_C. IPR013158. APOBEC_N. IPR016193. Cytidine_deaminase-like. [Graphical view]
KO	K01500.
Pfam	PF05240. APOBEC_C. 2 hits. PF08210. APOBEC_N. 2 hits. [Graphical view]
SUPFAM	SSF53927. Cytidine_deaminase-like. 2 hits.
PROSITE	PS00903. CYT_DCMP_DEAMINASES. 2 hits. [Graphical view]
ProtoNet	Search...
Other
NextBio	89891.
SOURCE	Search...

Entry information

Entry name

ABC3F_HUMAN

Accession

Primary (citable) accession number: Q8IUX4
Secondary accession number(s): B0QYD4 , Q45F03, Q7Z2N2, Q7Z2N5

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2004
Last sequence update:	October 23, 2007
Last modified:	January 25, 2012
This is version 81 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.