APOBEC3F (Kr.22q13.1), A3F

APOBEC3F

https://www.ncbi.nlm.nih.gov/gene/200316

Also known as A3F; KA6; ARP8; BK150C2.4.MRNA

Summary This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

Expression Broad expression in lymph node (RPKM 2.8), ovary (RPKM 2.8) and 24 other tissues See more Orthologs all

Preferred Names

DNA dC->dU-editing enzyme APOBEC-3F

Names

apolipoprotein B editing enzyme catalytic polypeptide-like 3F

apolipoprotein B mRNA editing enzyme cytidine deaminase

apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F

induced upon T-cell activation

Peptide sequence and history

https://www.ncbi.nlm.nih.gov/protein/NP_001006667.1

Related articles in PubMed

1. Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia. An P, et al. PLoS Genet, 2016 Mar. PMID 26942578, Free PMC Article Human APOBEC3 cytidine deaminases are intrinsic resistance factors to HIV-1. However, HIV-1 encodes a viral infectivity factor (Vif) that degrades APOBEC3 proteins. In vitro APOBEC3F (A3F) anti-HIV-1 activity is weaker than A3G but is partially resistant to Vif degradation unlike A3G. It is unknown whether A3F protein affects HIV-1 disease in vivo. To assess the effect of A3F gene on host susceptibility to HIV- acquisition and disease progression, we performed a genetic association study in six well-characterized HIV-1 natural cohorts. A common six-Single Nucleotide Polymorphism (SNP) haplotype of A3F tagged by a codon-changing variant (p. I231V, with allele (V) frequency of 48% in European Americans) was associated with significantly lower set-point viral load and slower rate of progression to AIDS (Relative Hazards (RH) = 0.71, 95% CI: 0.56, 0.91) and delayed development of pneumocystis pneumonia (PCP) (RH = 0.53, 95% CI: 0.37-0.76). A validation study in the International Collaboration for the Genomics of HIV (ICGH) showed a consistent association with lower set-point viral load. An in vitro assay revealed that the A3F I231V variant may influence Vif mediated A3F degradation. Our results provide genetic epidemiological evidence that A3F modulates HIV-1/AIDS disease progression.
2. Overexpression of APOBEC3F in tumor tissues is potentially predictive for poor recurrence-free survival from HBV-related hepatocellular carcinoma. Yang Z, et al. Discov Med, 2015 Dec. PMID 26760979
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338907/
   Genetic analysis of the localization of APOBEC3F to human immunodeficiency virus type 1 virion cores. Donahue JP, et al. J Virol, 2015 Feb. PMID 25505075, Free PMC Article IMPORTANCE: Specific leucine-leucine interactions are identified as necessary for A3F's core localization and anti-HIV activity but not for its packaging into virions. Understanding these signals may lead to novel strategies to enhance core localization that may augment effects of A3F against HIV and perhaps of other A3s against retroviruses, parvoviruses, and hepatitis B virus.
4. [Structure analysis of apolipoprotein B 3' variable number of tandem repeats]. Du G, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2006 Jun. PMID 16767679
5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5244329/ Mechanism of Enhanced HIV Restriction by Virion Coencapsidated Cytidine Deaminases APOBEC3F and APOBEC3G. Ara A, et al. J Virol, 2017 Feb 1. PMID 27881650, Free PMC Article
   

See all (192) citations in PubMed

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

1. APOBEC3DE binds to itself, APOBEC3F, and APOBEC3G and antagonizes APOBEC3F and, to a lesser extent, APOBEC3G restriction of hepatitis B virus replication.
2. These results indicate that APOBEC3 proteins can be copackaged and can comutate the same genomes, and can cooperate to inhibit HIV replication.
3. an APOBEC3F/APOBEC3G hetero-oligomer can form that has unique properties compared to each APOBEC3 alone. This hetero-oligomer has increased efficiency of virus hypermutation, raising the idea that we still may not fully realize the antiviral mechanisms of endogenous APOBEC3 enzymes. Hetero-oligomerization may be a mechanism to increase their antiviral activity in the presence of Vif.
4. virus adaptation and computational studies to interrogate the APOBEC3F-Vif interface and build a robust structural model; taken together with mutagenesis results, propose a wobble model to explain how HIV-1 Vif has evolved to bind different APOBEC3 enzymes
5. Findings support a role for APOBEC3G/F proteins in the generation of plasma drug-resistant minority human immunodeficiency virus type 1 variants (DRMVs). However, this role seems to be limited to a small subset of mutations and does not explain most of the DRMVs evaluated.
6. Overexpression of APOBEC3F in tumor tissues is potentially predictive for poor recurrence-free survival from hepatitis b virus-hepatocellular carcinoma patients.
7. Our results provide genetic epidemiological evidence that A3F(APOBEC3F ) modulates HIV-1/AIDS disease progression
8. https://www.ncbi.nlm.nih.gov/pubmed/26537685
   Six residues located within the conserved HIV-1 Vif F1-, F2-, and F3-box motifs are essential for both APOBEC3C and APOBEC3F degradation, and an additional four residues are uniquely required for APOBEC3F degradation.
9. This study showed for the first time a high level of APOBEC3F/3G editing in HIV-2 sequences from antiretroviral-naive patients. Compared with HIV-1 Vif sequences, a higher number of Vif defective sequences was observed in HIV-2 group A (P = 0.00001) and group B sequences (P = 0.013).CONCLUSION: We showed for the first time a high level of APOBEC3F/3G editing in HIV-2 sequences from antiretroviral-naive patients. Our study reported a group effect with a significantly higher level of APOBEC3F/3G editing in HIV-2 group B than in group A sequences.
10. APOBEC3D/F and APOBEC3G fundamentally work as restriction factors against HIV-1 in vivo
    

Peptidesequence and history

DNA dC->dU-editing enzyme APOBEC-3F isoform b [Homo sapiens]

NCBI Reference Sequence: NP_001006667.1
Identical Proteins FASTA Graphics

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LOCUS       NP_001006667             101 aa            linear   PRI 09-MAY-2018
DEFINITION  DNA dC->dU-editing enzyme APOBEC-3F isoform b [Homo sapiens].
ACCESSION   NP_001006667
VERSION     NP_001006667.1
DBSOURCE    REFSEQ: accession NM_001006666.1
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (residues 1 to 101)
  AUTHORS   Ara A, Love RP, Follack TB, Ahmed KA, Adolph MB and Chelico L.
  TITLE     Mechanism of Enhanced HIV Restriction by Virion Coencapsidated
            Cytidine Deaminases APOBEC3F and APOBEC3G
  JOURNAL   J. Virol. 91 (3), e02230-16 (2017)
   PUBMED   27881650
  REMARK    GeneRIF: an APOBEC3F/APOBEC3G hetero-oligomer can form that has
            unique properties compared to each APOBEC3 alone. This
            hetero-oligomer has increased efficiency of virus hypermutation,
            raising the idea that we still may not fully realize the antiviral
            mechanisms of endogenous APOBEC3 enzymes. Hetero-oligomerization
            may be a mechanism to increase their antiviral activity in the
            presence of Vif.
            Publication Status: Online-Only
REFERENCE   2  (residues 1 to 101)
  AUTHORS   Desimmie BA, Burdick RC, Izumi T, Doi H, Shao W, Alvord WG, Sato K,
            Koyanagi Y, Jones S, Wilson E, Hill S, Maldarelli F, Hu WS and
            Pathak VK.
  TITLE     APOBEC3 proteins can copackage and comutate HIV-1 genomes
  JOURNAL   Nucleic Acids Res. 44 (16), 7848-7865 (2016)
   PUBMED   27439715
  REMARK    GeneRIF: These results indicate that APOBEC3 proteins can be
            copackaged and can comutate the same genomes, and can cooperate to
            inhibit HIV replication.
REFERENCE   3  (residues 1 to 101)
  AUTHORS   Bouzidi MS, Caval V, Suspene R, Hallez C, Pineau P, Wain-Hobson S
            and Vartanian JP.
  TITLE     APOBEC3DE Antagonizes Hepatitis B Virus Restriction Factors
            APOBEC3F and APOBEC3G
  JOURNAL   J. Mol. Biol. 428 (17), 3514-3528 (2016)
   PUBMED   27289067
  REMARK    GeneRIF: APOBEC3DE binds to itself, APOBEC3F, and APOBEC3G and
            antagonizes APOBEC3F and, to a lesser extent, APOBEC3G restriction
            of hepatitis B virus replication.
REFERENCE   4  (residues 1 to 101)
  AUTHORS   An P, Penugonda S, Thorball CW, Bartha I, Goedert JJ, Donfield S,
            Buchbinder S, Binns-Roemer E, Kirk GD, Zhang W, Fellay J, Yu XF and
            Winkler CA.
  TITLE     Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and
            Pneumocystis Pneumonia
  JOURNAL   PLoS Genet. 12 (3), e1005921 (2016)
   PUBMED   26942578
  REMARK    GeneRIF: Our results provide genetic epidemiological evidence that
            A3F(APOBEC3F ) modulates HIV-1/AIDS disease progression
            Publication Status: Online-Only
REFERENCE   5  (residues 1 to 101)
  AUTHORS   Yang Z, Zhuang L, Yu Y, Zhou W, Lu Y, Xu Q, Tang B and Chen X.
  TITLE     Overexpression of APOBEC3F in tumor tissues is potentially
            predictive for poor recurrence-free survival from HBV-related
            hepatocellular carcinoma
  JOURNAL   Discov Med 20 (112), 349-356 (2015)
   PUBMED   26760979
  REMARK    GeneRIF: Overexpression of APOBEC3F in tumor tissues is potentially
            predictive for poor recurrence-free survival from hepatitis b
            virus-hepatocellular carcinoma patients.
REFERENCE   6  (residues 1 to 101)
  AUTHORS   Zhang H, Yang B, Pomerantz RJ, Zhang C, Arunachalam SC and Gao L.
  TITLE     The cytidine deaminase CEM15 induces hypermutation in newly
            synthesized HIV-1 DNA
  JOURNAL   Nature 424 (6944), 94-98 (2003)
   PUBMED   12808465
REFERENCE   7  (residues 1 to 101)
  AUTHORS   Wedekind JE, Dance GS, Sowden MP and Smith HC.
  TITLE     Messenger RNA editing in mammals: new members of the APOBEC family
            seeking roles in the family business
  JOURNAL   Trends Genet. 19 (4), 207-216 (2003)
   PUBMED   12683974
  REMARK    Review article
            Erratum:[Trends Genet. 2003 Jul;19(7):369]
REFERENCE   8  (residues 1 to 101)
  AUTHORS   Sheehy AM, Gaddis NC, Choi JD and Malim MH.
  TITLE     Isolation of a human gene that inhibits HIV-1 infection and is
            suppressed by the viral Vif protein
  JOURNAL   Nature 418 (6898), 646-650 (2002)
   PUBMED   12167863
REFERENCE   9  (residues 1 to 101)
  AUTHORS   Jarmuz A, Chester A, Bayliss J, Gisbourne J, Dunham I, Scott J and
            Navaratnam N.
  TITLE     An anthropoid-specific locus of orphan C to U RNA-editing enzymes
            on chromosome 22
  JOURNAL   Genomics 79 (3), 285-296 (2002)
   PUBMED   11863358
REFERENCE   10 (residues 1 to 101)
  AUTHORS   Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE,
            Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida
            JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O,
            Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD,
            O'Brien KP et al.
  TITLE     The DNA sequence of human chromosome 22
  JOURNAL   Nature 402 (6761), 489-495 (1999)
   PUBMED   10591208
  REMARK    Erratum:[Nature 2000 Apr 20;404(6780):904]
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BQ056344.1, CR456395.1 and
            BM681311.1.
            
            Summary: This gene is a member of the cytidine deaminase gene
            family. It is one of seven related genes or pseudogenes found in a
            cluster, thought to result from gene duplication, on chromosome 22.
            Members of the cluster encode proteins that are structurally and
            functionally related to the C to U RNA-editing cytidine deaminase
            APOBEC1. It is thought that the proteins may be RNA editing enzymes
            and have roles in growth or cell cycle control. Alternatively
            spliced transcript variants encoding different isoforms have been
            identified. [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (2) contains a distinct 3' UTR and
            3' coding region, compared to variant 1. The resulting isoform (b)
            is shorter and has a distinct C-terminus when compared to isoform
            a.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BF508948.1, SRR1163657.325175.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..101
                     /organism="Homo sapiens"
                     /db_xref="taxon:9606"
                     /chromosome="22"
                     /map="22q13.1"
     Protein         1..101
                     /product="DNA dC->dU-editing enzyme APOBEC-3F isoform b"
                     /note="induced upon T-cell activation; DNA dC->dU-editing
                     enzyme APOBEC-3F; apolipoprotein B mRNA-editing enzyme
                     catalytic polypeptide-like 3F; apolipoprotein B mRNA
                     editing enzyme cytidine deaminase; apolipoprotein B
                     editing enzyme catalytic polypeptide-like 3F"
                     /calculated_mol_wt=11691
     Region          17..>88
                     /region_name="APOBEC_N"
                     /note="APOBEC-like N-terminal domain; pfam08210"
                     /db_xref="CDD:285428"
     CDS             1..101
                     /gene="APOBEC3F"
                     /gene_synonym="A3F; ARP8; BK150C2.4.MRNA; KA6"
                     /coded_by="NM_001006666.1:294..599"
                     /note="isoform b is encoded by transcript variant 2"
                     /db_xref="CCDS:CCDS33649.1"
                     /db_xref="GeneID:200316"
                     /db_xref="HGNC:HGNC:17356"
                     /db_xref="MIM:608993"
ORIGIN      
        1 mkphfrntve rmyrdtfsyn fynrpilsrr ntvwlcyevk tkgpsrprld akifrgqvpr
       61 sfirapfqvl sspfgqcapp hgtaqvqwpp qltagreqgr p
//