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Q9UH17 (ABC3B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA dC->dU-editing enzyme APOBEC-3B

Short name=A3B
EC=3.5.4.-
Alternative name(s):
Phorbolin-1-related protein
Phorbolin-2/3
Gene names
Name:APOBEC3B
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length382 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination-independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double-stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Ref.2 Ref.8 Ref.9 Ref.10 Ref.17 Ref.20

Catalytic activity

Cytidine + H2O = uridine + NH3.

Cofactor

Zinc.

Subunit structure

Homodimer. Interacts with APOBEC3G. Does not interact with APOBEC1. Ref.6

Subcellular location

Nucleus Ref.12 Ref.15 Ref.18 Ref.21.

Tissue specificity

Expressed at high and moderate levels in peripheral blood leukocytes, spleen, testes, heart, thymus, prostate and ovary. Also expressed at low levels in several other tissues. Ref.6 Ref.16

Induction

Phorbol 12-myristate 13-acetate (PMA) induces overexpression in keratinocytes. Up-regulated by IFN-alpha. Ref.1

Domain

The CMP/dCMP deaminase zinc-binding 1 domain mediates RNA binding, RNA-dependent oligomerization and virion incorporation whereas the CMP/dCMP deaminase zinc-binding 2 domain confers deoxycytidine deaminase activity and substrate sequence specificity (Ref.11). Ref.11

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.

Contains 2 CMP/dCMP deaminase zinc-binding domains.

Sequence caution

The sequence AAD00089.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAD00090.1 differs from that shown. Reason: Frameshift at positions 59 and 134. Frameshifts result in two separate ORFs termed phorbolins 2 and 3.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UH17-1)

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: Q9UH17-2)

The sequence of this isoform differs from the canonical sequence as follows:
     191-382: YLMDPDTFTF...LRAILQNQGN → LRIFSVAFTA...CVRSFRRTHT
Note: May be due to a competing donor splice site.
Isoform 3 (identifier: Q9UH17-3)

The sequence of this isoform differs from the canonical sequence as follows:
     242-266: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 382382DNA dC->dU-editing enzyme APOBEC-3B
PRO_0000171753

Regions

Domain66 – 10035CMP/dCMP deaminase zinc-binding 1
Domain253 – 28937CMP/dCMP deaminase zinc-binding 2

Sites

Active site2551Proton donor Potential
Metal binding661Zinc By similarity
Metal binding971Zinc By similarity
Metal binding1001Zinc By similarity
Metal binding2531Zinc By similarity
Metal binding2841Zinc By similarity
Metal binding2891Zinc By similarity

Natural variations

Alternative sequence191 – 382192YLMDP…QNQGN → LRIFSVAFTAAMRSCASWTW FLLCSWTRPRSTGSLGSSPG APASPGAVPGKCVRSFRRTH T in isoform 2.
VSP_009802
Alternative sequence242 – 26625Missing in isoform 3.
VSP_044900
Natural variant621K → E. Ref.3
Corresponds to variant rs2076109 [ dbSNP | Ensembl ].
VAR_018142
Natural variant981P → L.
Corresponds to variant rs2076110 [ dbSNP | Ensembl ].
VAR_018143
Natural variant1091S → A.
Corresponds to variant rs17000697 [ dbSNP | Ensembl ].
VAR_033455
Natural variant1461T → K. Ref.1 Ref.3 Ref.5
Corresponds to variant rs5995649 [ dbSNP | Ensembl ].
VAR_018144
Natural variant3511R → H.
Corresponds to variant rs1053813 [ dbSNP | Ensembl ].
VAR_048722

Experimental info

Sequence conflict103 – 1042KL → NV in AAD00090. Ref.1
Sequence conflict227 – 2282TW → WM in AAD00089. Ref.1
Sequence conflict255 – 2562EL → DW in AAD00089. Ref.1
Sequence conflict3061R → P in AAD00089. Ref.1
Sequence conflict3561F → S in AAW31743. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: DA6EDD23E8856240

FASTA38245,924
        10         20         30         40         50         60 
MNPQIRNPME RMYRDTFYDN FENEPILYGR SYTWLCYEVK IKRGRSNLLW DTGVFRGQVY 

        70         80         90        100        110        120 
FKPQYHAEMC FLSWFCGNQL PAYKCFQITW FVSWTPCPDC VAKLAEFLSE HPNVTLTISA 

       130        140        150        160        170        180 
ARLYYYWERD YRRALCRLSQ AGARVTIMDY EEFAYCWENF VYNEGQQFMP WYKFDENYAF 

       190        200        210        220        230        240 
LHRTLKEILR YLMDPDTFTF NFNNDPLVLR RRQTYLCYEV ERLDNGTWVL MDQHMGFLCN 

       250        260        270        280        290        300 
EAKNLLCGFY GRHAELRFLD LVPSLQLDPA QIYRVTWFIS WSPCFSWGCA GEVRAFLQEN 

       310        320        330        340        350        360 
THVRLRIFAA RIYDYDPLYK EALQMLRDAG AQVSIMTYDE FEYCWDTFVY RQGCPFQPWD 

       370        380 
GLEEHSQALS GRLRAILQNQ GN 

« Hide

Isoform 2 [UniParc].

Checksum: 9F2B8220F6689383
Show »

FASTA25129,798
Isoform 3 [UniParc].

Checksum: C2666AD355F1D771
Show »

FASTA35743,081

References

« Hide 'large scale' references
[1]"Psoriasis upregulated phorbolin-1 shares structural but not functional similarity to the mRNA-editing protein apobec-1."
Madsen P.P., Anant S., Rasmussen H.H., Gromov P., Vorum H., Dumanski J.P., Tommerup N., Collins J.E., Wright C.L., Dunham I., Macginnitie A.J., Davidson N.O., Celis J.E.
J. Invest. Dermatol. 113:162-169(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), VARIANT LYS-146, INDUCTION.
Tissue: Keratinocyte.
[2]"Regulated production and anti-HIV type 1 activities of cytidine deaminases APOBEC3B, 3F, and 3G."
Rose K.M., Marin M., Kozak S.L., Kabat D.
AIDS Res. Hum. Retroviruses 21:611-619(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION.
[3]"A genome annotation-driven approach to cloning the human ORFeome."
Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I.
Genome Biol. 5:R84.1-R84.11(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3), VARIANTS GLU-62 AND LYS-146.
[4]"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. expand/collapse author list , 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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT LYS-146.
Tissue: Uterus.
[6]"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] [Europe PMC] [Abstract]
Cited for: GENE FAMILY ORGANIZATION, TISSUE SPECIFICITY, RNA-BINDING, ZINC-BINDING, INTERACTION WITH APOBEC3G.
[7]"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] [Europe PMC] [Abstract]
Cited for: REVIEW ON APOBEC FAMILIES.
[8]"Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif."
Mariani R., Chen D., Schroefelbauer B., Navarro F., Koenig R., Bollman B., Muenk C., Nymark-McMahon H., Landau N.R.
Cell 114:21-31(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN HIV-1 INFECTIVITY.
[9]"APOBEC3B and APOBEC3C are potent inhibitors of simian immunodeficiency virus replication."
Yu Q., Chen D., Koenig R., Mariani R., Unutmaz D., Landau N.R.
J. Biol. Chem. 279:53379-53386(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SIV RESTRICTION.
[10]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION IN RETROTRANSPOSITION.
[11]"Reversed functional organization of mouse and human APOBEC3 cytidine deaminase domains."
Hakata Y., Landau N.R.
J. Biol. Chem. 281:36624-36631(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: DOMAIN CMP/DCMP DEAMINASE ZINC-BINDING.
[12]"Human retroviral host restriction factors APOBEC3G and APOBEC3F localize to mRNA processing bodies."
Wichroski M.J., Robb G.B., Rana T.M.
PLoS Pathog. 2:E41-E41(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[13]"The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements."
Chiu Y.L., Greene W.C.
Annu. Rev. Immunol. 26:317-353(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[14]"Hepatitis B: modern concepts in pathogenesis--APOBEC3 cytidine deaminases as effectors in innate immunity against the hepatitis B virus."
Bonvin M., Greeve J.
Curr. Opin. Infect. Dis. 21:298-303(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW ON FUNCTION IN HBV RESTRICTION.
[15]"Two regions within the amino-terminal half of APOBEC3G cooperate to determine cytoplasmic localization."
Stenglein M.D., Matsuo H., Harris R.S.
J. Virol. 82:9591-9599(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[16]"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] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
[17]"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] [Europe PMC] [Abstract]
Cited for: FUNCTION IN RETROTRANSPOSITION.
[18]"Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1."
Hultquist J.F., Lengyel J.A., Refsland E.W., LaRue R.S., Lackey L., Brown W.L., Harris R.S.
J. Virol. 85:11220-11234(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[19]"Retroelements versus APOBEC3 family members: No great escape from the magnificent seven."
Arias J.F., Koyama T., Kinomoto M., Tokunaga K.
Front. Microbiol. 3:275-275(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[20]"APOBEC3A, APOBEC3B, and APOBEC3H haplotype 2 restrict human T-lymphotropic virus type 1."
Ooms M., Krikoni A., Kress A.K., Simon V., Muenk C.
J. Virol. 86:6097-6108(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN HTLV-1 RESTRICTION.
[21]"HIV-1 replication and APOBEC3 antiviral activity are not regulated by P bodies."
Phalora P.K., Sherer N.M., Wolinsky S.M., Swanson C.M., Malim M.H.
J. Virol. 86:11712-11724(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.
[22]"Functions and regulation of the APOBEC family of proteins."
Smith H.C., Bennett R.P., Kizilyer A., McDougall W.M., Prohaska K.M.
Semin. Cell Dev. Biol. 23:258-268(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U61083 mRNA. Translation: AAD00089.1. Different initiation.
U61084 mRNA. Translation: AAD00090.1. Frameshift.
AY743217 mRNA. Translation: AAW31743.1.
CT841510 mRNA. Translation: CAJ86440.1.
AL022318 Genomic DNA. Translation: CAB45270.1.
AL022318 Genomic DNA. Translation: CAQ09851.1.
BC053859 mRNA. Translation: AAH53859.1.
RefSeqNP_001257340.1. NM_001270411.1.
NP_004891.4. NM_004900.4.
UniGeneHs.226307.
Hs.658626.

3D structure databases

ProteinModelPortalQ9UH17.
SMRQ9UH17. Positions 4-382.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114950. 1 interaction.
IntActQ9UH17. 3 interactions.
MINTMINT-4992727.
STRING9606.ENSP00000327459.

PTM databases

PhosphoSiteQ9UH17.

Polymorphism databases

DMDM12643884.

Proteomic databases

PaxDbQ9UH17.
PRIDEQ9UH17.

Protocols and materials databases

DNASU9582.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000333467; ENSP00000327459; ENSG00000179750. [Q9UH17-1]
ENST00000335760; ENSP00000338897; ENSG00000179750. [Q9UH17-2]
ENST00000407298; ENSP00000385068; ENSG00000179750. [Q9UH17-3]
GeneID9582.
KEGGhsa:9582.
UCSCuc003awo.2. human. [Q9UH17-1]
uc003awp.2. human.

Organism-specific databases

CTD9582.
GeneCardsGC22P039378.
HGNCHGNC:17352. APOBEC3B.
MIM607110. gene.
neXtProtNX_Q9UH17.
PharmGKBPA24892.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG135704.
HOGENOMHOG000033755.
HOVERGENHBG050434.
KOK01500.
OrthoDBEOG75QR3Z.
PhylomeDBQ9UH17.
TreeFamTF331356.

Gene expression databases

ArrayExpressQ9UH17.
BgeeQ9UH17.
CleanExHS_APOBEC3B.
GenevestigatorQ9UH17.

Family and domain databases

InterProIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR007904. APOBEC_C.
IPR013158. APOBEC_N.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamPF05240. APOBEC_C. 1 hit.
PF08210. APOBEC_N. 1 hit.
[Graphical view]
SUPFAMSSF53927. SSF53927. 2 hits.
PROSITEPS00903. CYT_DCMP_DEAMINASES. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiAPOBEC3B.
GenomeRNAi9582.
NextBio35465727.
PROQ9UH17.
SOURCESearch...

Entry information

Entry nameABC3B_HUMAN
AccessionPrimary (citable) accession number: Q9UH17
Secondary accession number(s): B0QYD2 expand/collapse secondary AC list , O95618, Q20WL1, Q5IFJ4, Q7Z2N3, Q7Z6D6, Q9UE74
Entry history
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: May 1, 2000
Last modified: April 16, 2014
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 22

Human chromosome 22: entries, gene names and cross-references to MIM