Reviewed, UniProtKB/Swiss-Prot Q8IUX4 (ABC3F_HUMAN)

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) [Complete proteome]

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.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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. Ref.7
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.
Tissue specificity	Widely expressed, including in lymphoid tissues, such as thymus and peripheral blood leukocytes. No expression detected in permissive lymphoid. Ref.7 Ref.5
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
Coding sequence diversity	Alternative splicing Polymorphism
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	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 positive regulation of defense response to virus by host Inferred from direct assay. Source: HGNC transcription, RNA-dependent Inferred from direct assay. Source: HGNC
Cellular component	apolipoprotein B mRNA editing enzyme complex Traceable author statement. Source: HGNC
Molecular function	RNA binding Ref.5 Inferred from direct assay. Source: HGNC cytidine deaminase activity Inferred from direct assay. Source: HGNC zinc ion binding Ref.5 Inferred from direct assay. 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: dbSNP rs35053197. Ref.4		VAR_038355
	Natural variant	61	1	Q → L: dbSNP rs2076109.		VAR_018145
	Natural variant	97	1	P → L: dbSNP rs2076110.		VAR_018146
	Natural variant	108	1	A → S: dbSNP rs2020390. Ref.4		VAR_018147
	Natural variant	178	1	A → T: dbSNP rs34182094.		VAR_025058
	Natural variant	231	1	V → I: dbSNP rs2076101. Ref.1		VAR_018148
	Natural variant	307	1	Y → C: dbSNP rs12157816. Ref.1		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. 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.
+	Additional computationally mapped references.

Web resources

SeattleSNPs

Cross-references

Sequence databases
EMBLGenBankDDBJ	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.
UniGene	Hs.659809 Hs.660143
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	Q8IUX4.
Proteomic databases
PRIDE	Q8IUX4.
Genome annotation databases
Ensembl	ENST00000308521; ENSP00000309749; ENSG00000128394; Homo sapiens. [Genome view]
GeneID	200316.
NMPDR	fig|9606.3.peg.21730.
UCSC	uc003aww.1. human.
Organism-specific databases
CTD	200316.
GeneCards	GC22P037761.
HGNC	HGNC:17356. APOBEC3F.
MIM	608993. gene.
PharmGKB	PA24896.
GenAtlas	Search...
Phylogenomic databases
HOVERGEN	Q8IUX4.
OrthoDB	EOG934ZRM
Enzyme and pathway databases
BRENDA	3.5.4.5. 247.
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]
Pfam	PF05240. APOBEC_C. 2 hits. PF08210. APOBEC_N. 2 hits. [Graphical view]
PROSITE	PS00903. CYT_DCMP_DEAMINASES. 2 hits. [Graphical view]
ProtoNet	Search...
Other Resources
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:	November 24, 2009
This is version 62 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.