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Protein

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

Gene

APOBEC3B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.6 Publications

Miscellaneous

It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22.

Catalytic activityi

Cytidine + H2O = uridine + NH3.

Cofactori

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi66ZincBy similarity1
Metal bindingi97ZincBy similarity1
Metal bindingi100ZincBy similarity1
Metal bindingi253ZincBy similarity1
Active sitei255Proton donorSequence analysis1
Metal bindingi284ZincBy similarity1
Metal bindingi289ZincBy similarity1

GO - Molecular functioni

  • cytidine deaminase activity Source: GO_Central
  • deoxycytidine deaminase activity Source: UniProtKB
  • RNA binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionHydrolase, RNA-binding
Biological processAntiviral defense, Immunity, Innate immunity
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-72200 mRNA Editing: C to U Conversion
R-HSA-75094 Formation of the Editosome

Names & Taxonomyi

Protein namesi
Recommended name:
DNA dC->dU-editing enzyme APOBEC-3B (EC:3.5.4.-)
Short name:
A3B
Alternative name(s):
Phorbolin-1-related protein
Phorbolin-2/3
Gene namesi
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000179750.15
HGNCiHGNC:17352 APOBEC3B
MIMi607110 gene
neXtProtiNX_Q9UH17

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi9582
OpenTargetsiENSG00000179750
PharmGKBiPA24892

Polymorphism and mutation databases

BioMutaiAPOBEC3B
DMDMi12643884

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001717531 – 382DNA dC->dU-editing enzyme APOBEC-3BAdd BLAST382

Proteomic databases

EPDiQ9UH17
PaxDbiQ9UH17
PeptideAtlasiQ9UH17
PRIDEiQ9UH17
ProteomicsDBi84274
84275 [Q9UH17-2]

PTM databases

iPTMnetiQ9UH17
PhosphoSitePlusiQ9UH17

Expressioni

Tissue specificityi

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.2 Publications

Inductioni

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

Gene expression databases

BgeeiENSG00000179750 Expressed in 81 organ(s), highest expression level in mucosa of transverse colon
CleanExiHS_APOBEC3B
ExpressionAtlasiQ9UH17 baseline and differential
GenevisibleiQ9UH17 HS

Organism-specific databases

HPAiHPA056980
HPA066719

Interactioni

Subunit structurei

Homodimer. Interacts with APOBEC3G. Does not interact with APOBEC1.1 Publication

Protein-protein interaction databases

BioGridi114950, 74 interactors
IntActiQ9UH17, 17 interactors
STRINGi9606.ENSP00000327459

Structurei

Secondary structure

1382
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9UH17
SMRiQ9UH17
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 138CMP/dCMP-type deaminase 1PROSITE-ProRule annotationAdd BLAST110
Domaini210 – 326CMP/dCMP-type deaminase 2PROSITE-ProRule annotationAdd BLAST117

Domaini

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

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410JBA1 Eukaryota
ENOG41119MS LUCA
GeneTreeiENSGT00530000062933
HOGENOMiHOG000033755
HOVERGENiHBG050434
KOiK18750
PhylomeDBiQ9UH17
TreeFamiTF331356

Family and domain databases

InterProiView protein in InterPro
IPR016192 APOBEC/CMP_deaminase_Zn-bd
IPR013158 APOBEC_N
IPR002125 CMP_dCMP_dom
IPR016193 Cytidine_deaminase-like
PfamiView protein in Pfam
PF08210 APOBEC_N, 2 hits
SUPFAMiSSF53927 SSF53927, 2 hits
PROSITEiView protein in PROSITE
PS00903 CYT_DCMP_DEAMINASES_1, 2 hits
PS51747 CYT_DCMP_DEAMINASES_2, 2 hits

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: Q9UH17-1) [UniParc]FASTAAdd to basket

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.

« Hide
        10         20         30         40         50
MNPQIRNPME RMYRDTFYDN FENEPILYGR SYTWLCYEVK IKRGRSNLLW
60 70 80 90 100
DTGVFRGQVY FKPQYHAEMC FLSWFCGNQL PAYKCFQITW FVSWTPCPDC
110 120 130 140 150
VAKLAEFLSE HPNVTLTISA ARLYYYWERD YRRALCRLSQ AGARVTIMDY
160 170 180 190 200
EEFAYCWENF VYNEGQQFMP WYKFDENYAF LHRTLKEILR YLMDPDTFTF
210 220 230 240 250
NFNNDPLVLR RRQTYLCYEV ERLDNGTWVL MDQHMGFLCN EAKNLLCGFY
260 270 280 290 300
GRHAELRFLD LVPSLQLDPA QIYRVTWFIS WSPCFSWGCA GEVRAFLQEN
310 320 330 340 350
THVRLRIFAA RIYDYDPLYK EALQMLRDAG AQVSIMTYDE FEYCWDTFVY
360 370 380
RQGCPFQPWD GLEEHSQALS GRLRAILQNQ GN
Length:382
Mass (Da):45,924
Last modified:May 1, 2000 - v1
Checksum:iDA6EDD23E8856240
GO
Isoform 2 (identifier: Q9UH17-2) [UniParc]FASTAAdd to basket

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.
Show »
Length:251
Mass (Da):29,798
Checksum:i9F2B8220F6689383
GO
Isoform 3 (identifier: Q9UH17-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     242-266: Missing.

Note: No experimental confirmation available.
Show »
Length:357
Mass (Da):43,081
Checksum:iC2666AD355F1D771
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B0QYD3B0QYD3_HUMAN
DNA dC->dU-editing enzyme APOBEC-3B
APOBEC3B
490Annotation score:

Sequence cautioni

The sequence AAD00089 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAD00090 differs from that shown. Reason: Frameshift at positions 59 and 134. Frameshifts result in two separate ORFs termed phorbolins 2 and 3.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti103 – 104KL → NV in AAD00090 (PubMed:10469298).Curated2
Sequence conflicti227 – 228TW → WM in AAD00089 (PubMed:10469298).Curated2
Sequence conflicti255 – 256EL → DW in AAD00089 (PubMed:10469298).Curated2
Sequence conflicti306R → P in AAD00089 (PubMed:10469298).Curated1
Sequence conflicti356F → S in AAW31743 (PubMed:16060832).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01814262K → E1 PublicationCorresponds to variant dbSNP:rs2076109Ensembl.1
Natural variantiVAR_01814398P → L. Corresponds to variant dbSNP:rs2076110Ensembl.1
Natural variantiVAR_033455109S → A. Corresponds to variant dbSNP:rs17000697Ensembl.1
Natural variantiVAR_018144146T → K3 PublicationsCorresponds to variant dbSNP:rs5995649Ensembl.1
Natural variantiVAR_048722351R → H. Corresponds to variant dbSNP:rs1053813Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_009802191 – 382YLMDP…QNQGN → LRIFSVAFTAAMRSCASWTW FLLCSWTRPRSTGSLGSSPG APASPGAVPGKCVRSFRRTH T in isoform 2. 1 PublicationAdd BLAST192
Alternative sequenceiVSP_044900242 – 266Missing in isoform 3. 1 PublicationAdd BLAST25

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 No translation available.
BC053859 mRNA Translation: AAH53859.1
CCDSiCCDS13982.1 [Q9UH17-1]
CCDS58807.1 [Q9UH17-3]
RefSeqiNP_001257340.1, NM_001270411.1
NP_004891.4, NM_004900.4
UniGeneiHs.226307
Hs.658626

Genome annotation databases

EnsembliENST00000333467; ENSP00000327459; ENSG00000179750 [Q9UH17-1]
ENST00000335760; ENSP00000338897; ENSG00000179750 [Q9UH17-2]
ENST00000407298; ENSP00000385068; ENSG00000179750 [Q9UH17-3]
GeneIDi9582
KEGGihsa:9582
UCSCiuc003awo.3 human [Q9UH17-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 No translation available.
BC053859 mRNA Translation: AAH53859.1
CCDSiCCDS13982.1 [Q9UH17-1]
CCDS58807.1 [Q9UH17-3]
RefSeqiNP_001257340.1, NM_001270411.1
NP_004891.4, NM_004900.4
UniGeneiHs.226307
Hs.658626

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2NBQNMR-A187-382[»]
5CQDX-ray2.08A/C187-378[»]
5CQHX-ray1.73A187-378[»]
5CQIX-ray1.68A187-378[»]
5CQKX-ray1.88A187-378[»]
5SXGX-ray1.93A/B191-378[»]
5SXHX-ray1.78A/B191-378[»]
5TD5X-ray1.72A187-378[»]
5TKMX-ray1.90A/B1-191[»]
ProteinModelPortaliQ9UH17
SMRiQ9UH17
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114950, 74 interactors
IntActiQ9UH17, 17 interactors
STRINGi9606.ENSP00000327459

PTM databases

iPTMnetiQ9UH17
PhosphoSitePlusiQ9UH17

Polymorphism and mutation databases

BioMutaiAPOBEC3B
DMDMi12643884

Proteomic databases

EPDiQ9UH17
PaxDbiQ9UH17
PeptideAtlasiQ9UH17
PRIDEiQ9UH17
ProteomicsDBi84274
84275 [Q9UH17-2]

Protocols and materials databases

DNASUi9582
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000333467; ENSP00000327459; ENSG00000179750 [Q9UH17-1]
ENST00000335760; ENSP00000338897; ENSG00000179750 [Q9UH17-2]
ENST00000407298; ENSP00000385068; ENSG00000179750 [Q9UH17-3]
GeneIDi9582
KEGGihsa:9582
UCSCiuc003awo.3 human [Q9UH17-1]

Organism-specific databases

CTDi9582
DisGeNETi9582
EuPathDBiHostDB:ENSG00000179750.15
GeneCardsiAPOBEC3B
HGNCiHGNC:17352 APOBEC3B
HPAiHPA056980
HPA066719
MIMi607110 gene
neXtProtiNX_Q9UH17
OpenTargetsiENSG00000179750
PharmGKBiPA24892
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410JBA1 Eukaryota
ENOG41119MS LUCA
GeneTreeiENSGT00530000062933
HOGENOMiHOG000033755
HOVERGENiHBG050434
KOiK18750
PhylomeDBiQ9UH17
TreeFamiTF331356

Enzyme and pathway databases

ReactomeiR-HSA-72200 mRNA Editing: C to U Conversion
R-HSA-75094 Formation of the Editosome

Miscellaneous databases

GeneWikiiAPOBEC3B
GenomeRNAii9582
PROiPR:Q9UH17
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000179750 Expressed in 81 organ(s), highest expression level in mucosa of transverse colon
CleanExiHS_APOBEC3B
ExpressionAtlasiQ9UH17 baseline and differential
GenevisibleiQ9UH17 HS

Family and domain databases

InterProiView protein in InterPro
IPR016192 APOBEC/CMP_deaminase_Zn-bd
IPR013158 APOBEC_N
IPR002125 CMP_dCMP_dom
IPR016193 Cytidine_deaminase-like
PfamiView protein in Pfam
PF08210 APOBEC_N, 2 hits
SUPFAMiSSF53927 SSF53927, 2 hits
PROSITEiView protein in PROSITE
PS00903 CYT_DCMP_DEAMINASES_1, 2 hits
PS51747 CYT_DCMP_DEAMINASES_2, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiABC3B_HUMAN
AccessioniPrimary (citable) accession number: Q9UH17
Secondary accession number(s): B0QYD2
, O95618, Q20WL1, Q5IFJ4, Q7Z2N3, Q7Z6D6, Q9UE74
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: May 1, 2000
Last modified: November 7, 2018
This is version 151 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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