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Protein

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

Gene

APOBEC3B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

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

  • deoxycytidine deaminase activity Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • defense response to virus Source: UniProtKB
  • innate immune response Source: UniProtKB-KW
  • negative regulation of transposition Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Antiviral defense, Immunity, Innate immunity

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000179750-MONOMER.
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

HGNCiHGNC:17352. APOBEC3B.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: UniProtKB
Complete GO annotation...

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.

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.
CleanExiHS_APOBEC3B.
ExpressionAtlasiQ9UH17. baseline and differential.
GenevisibleiQ9UH17. HS.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi114950. 15 interactors.
IntActiQ9UH17. 15 interactors.
MINTiMINT-4992727.
STRINGi9606.ENSP00000327459.

Structurei

Secondary structure

1382
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni188 – 190Combined sources3
Helixi195 – 202Combined sources8
Beta strandi215 – 224Combined sources10
Beta strandi227 – 230Combined sources4
Helixi232 – 234Combined sources3
Beta strandi236 – 239Combined sources4
Helixi245 – 247Combined sources3
Helixi254 – 261Combined sources8
Helixi262 – 265Combined sources4
Beta strandi269 – 271Combined sources3
Beta strandi273 – 281Combined sources9
Helixi289 – 299Combined sources11
Turni300 – 302Combined sources3
Beta strandi303 – 311Combined sources9
Helixi319 – 328Combined sources10
Beta strandi332 – 335Combined sources4
Helixi338 – 348Combined sources11
Helixi362 – 377Combined sources16

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[»]
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

Contains 2 CMP/dCMP-type deaminase domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410JBA1. Eukaryota.
ENOG41119MS. LUCA.
GeneTreeiENSGT00530000062933.
HOGENOMiHOG000033755.
HOVERGENiHBG050434.
KOiK18750.
PhylomeDBiQ9UH17.
TreeFamiTF331356.

Family and domain databases

InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR013158. APOBEC_N.
IPR002125. CMP_dCMP_Zn-bd.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamiPF08210. APOBEC_N. 2 hits.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 2 hits.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 2 hits.
PS51747. CYT_DCMP_DEAMINASES_2. 2 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

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

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 → E.1 PublicationCorresponds to variant rs2076109dbSNPEnsembl.1
Natural variantiVAR_01814398P → L.Corresponds to variant rs2076110dbSNPEnsembl.1
Natural variantiVAR_033455109S → A.Corresponds to variant rs17000697dbSNPEnsembl.1
Natural variantiVAR_018144146T → K.3 PublicationsCorresponds to variant rs5995649dbSNPEnsembl.1
Natural variantiVAR_048722351R → H.Corresponds to variant rs1053813dbSNPEnsembl.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. Translation: CAB45270.1.
AL022318 Genomic DNA. Translation: CAQ09851.1.
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

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. Translation: CAB45270.1.
AL022318 Genomic DNA. Translation: CAQ09851.1.
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[»]
ProteinModelPortaliQ9UH17.
SMRiQ9UH17.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114950. 15 interactors.
IntActiQ9UH17. 15 interactors.
MINTiMINT-4992727.
STRINGi9606.ENSP00000327459.

PTM databases

iPTMnetiQ9UH17.
PhosphoSitePlusiQ9UH17.

Polymorphism and mutation databases

BioMutaiAPOBEC3B.
DMDMi12643884.

Proteomic databases

EPDiQ9UH17.
PaxDbiQ9UH17.
PeptideAtlasiQ9UH17.
PRIDEiQ9UH17.

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.
GeneCardsiAPOBEC3B.
HGNCiHGNC:17352. APOBEC3B.
MIMi607110. gene.
neXtProtiNX_Q9UH17.
OpenTargetsiENSG00000179750.
PharmGKBiPA24892.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410JBA1. Eukaryota.
ENOG41119MS. LUCA.
GeneTreeiENSGT00530000062933.
HOGENOMiHOG000033755.
HOVERGENiHBG050434.
KOiK18750.
PhylomeDBiQ9UH17.
TreeFamiTF331356.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000179750-MONOMER.
ReactomeiR-HSA-72200. mRNA Editing: C to U Conversion.
R-HSA-75094. Formation of the Editosome.

Miscellaneous databases

GeneWikiiAPOBEC3B.
GenomeRNAii9582.
PROiQ9UH17.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000179750.
CleanExiHS_APOBEC3B.
ExpressionAtlasiQ9UH17. baseline and differential.
GenevisibleiQ9UH17. HS.

Family and domain databases

InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
IPR013158. APOBEC_N.
IPR002125. CMP_dCMP_Zn-bd.
IPR016193. Cytidine_deaminase-like.
[Graphical view]
PfamiPF08210. APOBEC_N. 2 hits.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 2 hits.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 2 hits.
PS51747. CYT_DCMP_DEAMINASES_2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiABC3B_HUMAN
AccessioniPrimary (citable) accession number: Q9UH17
Secondary accession number(s): B0QYD2
, O95618, Q20WL1, Q5IFJ4, Q7Z2N3, Q7Z6D6, Q9UE74
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 140 of the entry and version 1 of the sequence. [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

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.