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Protein

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

Gene

APOBEC3D

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. Exhibits antiviral activity against vif-deficient HIV-1. 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. 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

Zn2+By similarity

Activity regulationi

Antiviral activity is neutralized by the HIV-1 virion infectivity factor (VIF), that prevents its incorporation into progeny virions by both inhibiting its translation and/or by inducing its ubiquitination and subsequent degradation by the 26S proteasome.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi78ZincBy similarity1
Metal bindingi109ZincBy similarity1
Metal bindingi112ZincBy similarity1
Metal bindingi262ZincBy similarity1
Active sitei264Proton donorBy similarity1
Metal bindingi293ZincBy similarity1
Metal bindingi296ZincBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA dC->dU-editing enzyme APOBEC-3D (EC:3.5.4.-)
Short name:
A3D
Gene namesi
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000243811.7
HGNCiHGNC:17354 APOBEC3D
MIMi609900 gene
neXtProtiNX_Q96AK3

Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi140564
OpenTargetsiENSG00000243811
PharmGKBiPA24894

Polymorphism and mutation databases

DMDMi48474596

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001717561 – 386DNA dC->dU-editing enzyme APOBEC-3DAdd BLAST386

Proteomic databases

EPDiQ96AK3
MaxQBiQ96AK3
PaxDbiQ96AK3
PeptideAtlasiQ96AK3
PRIDEiQ96AK3
ProteomicsDBi75971

PTM databases

iPTMnetiQ96AK3
PhosphoSitePlusiQ96AK3

Expressioni

Tissue specificityi

Expressed in lymphoid organs. Also detected in non-lymphoid tissues including lung.1 Publication

Gene expression databases

BgeeiENSG00000243811 Expressed in 94 organ(s), highest expression level in lymph node
ExpressionAtlasiQ96AK3 baseline and differential
GenevisibleiQ96AK3 HS

Organism-specific databases

HPAiHPA055116

Interactioni

Protein-protein interaction databases

IntActiQ96AK3, 2 interactors
STRINGi9606.ENSP00000216099

Structurei

3D structure databases

ProteinModelPortaliQ96AK3
SMRiQ96AK3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 145CMP/dCMP-type deaminase 1PROSITE-ProRule annotationAdd BLAST117
Domaini187 – 334CMP/dCMP-type deaminase 2PROSITE-ProRule annotationAdd BLAST148

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.

Sequence similaritiesi

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG410JBA1 Eukaryota
ENOG41119MS LUCA
GeneTreeiENSGT00530000062933
HOGENOMiHOG000033755
HOVERGENiHBG050434
OMAiFEYCWDN
OrthoDBiEOG091G07EI
PhylomeDBiQ96AK3
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

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

Q96AK3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNPQIRNPME RMYRDTFYDN FENEPILYGR SYTWLCYEVK IKRGRSNLLW
60 70 80 90 100
DTGVFRGPVL PKRQSNHRQE VYFRFENHAE MCFLSWFCGN RLPANRRFQI
110 120 130 140 150
TWFVSWNPCL PCVVKVTKFL AEHPNVTLTI SAARLYYYRD RDWRWVLLRL
160 170 180 190 200
HKAGARVKIM DYEDFAYCWE NFVCNEGQPF MPWYKFDDNY ASLHRTLKEI
210 220 230 240 250
LRNPMEAMYP HIFYFHFKNL LKACGRNESW LCFTMEVTKH HSAVFRKRGV
260 270 280 290 300
FRNQVDPETH CHAERCFLSW FCDDILSPNT NYEVTWYTSW SPCPECAGEV
310 320 330 340 350
AEFLARHSNV NLTIFTARLC YFWDTDYQEG LCSLSQEGAS VKIMGYKDFV
360 370 380
SCWKNFVYSD DEPFKPWKGL QTNFRLLKRR LREILQ
Length:386
Mass (Da):46,598
Last modified:December 1, 2001 - v1
Checksum:i94C7253BDCC85B22
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q6ICH2Q6ICH2_HUMAN
BK150C2.9 protein
APOBEC3D bK150C2.9, hCG_41704
202Annotation score:
A0A087WX48A0A087WX48_HUMAN
DNA dC->dU-editing enzyme APOBEC-3D
APOBEC3D
190Annotation score:

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL022318 Genomic DNA No translation available.
CCDSiCCDS46709.1
UniGeneiHs.629775
Hs.658626

Genome annotation databases

EnsembliENST00000216099; ENSP00000216099; ENSG00000243811
UCSCiuc003awt.5 human

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL022318 Genomic DNA No translation available.
CCDSiCCDS46709.1
UniGeneiHs.629775
Hs.658626

3D structure databases

ProteinModelPortaliQ96AK3
SMRiQ96AK3
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ96AK3, 2 interactors
STRINGi9606.ENSP00000216099

PTM databases

iPTMnetiQ96AK3
PhosphoSitePlusiQ96AK3

Polymorphism and mutation databases

DMDMi48474596

Proteomic databases

EPDiQ96AK3
MaxQBiQ96AK3
PaxDbiQ96AK3
PeptideAtlasiQ96AK3
PRIDEiQ96AK3
ProteomicsDBi75971

Protocols and materials databases

DNASUi140564
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000216099; ENSP00000216099; ENSG00000243811
UCSCiuc003awt.5 human

Organism-specific databases

DisGeNETi140564
EuPathDBiHostDB:ENSG00000243811.7
GeneCardsiAPOBEC3D
HGNCiHGNC:17354 APOBEC3D
HPAiHPA055116
MIMi609900 gene
neXtProtiNX_Q96AK3
OpenTargetsiENSG00000243811
PharmGKBiPA24894
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410JBA1 Eukaryota
ENOG41119MS LUCA
GeneTreeiENSGT00530000062933
HOGENOMiHOG000033755
HOVERGENiHBG050434
OMAiFEYCWDN
OrthoDBiEOG091G07EI
PhylomeDBiQ96AK3
TreeFamiTF331356

Miscellaneous databases

PROiPR:Q96AK3
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000243811 Expressed in 94 organ(s), highest expression level in lymph node
ExpressionAtlasiQ96AK3 baseline and differential
GenevisibleiQ96AK3 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 nameiABC3D_HUMAN
AccessioniPrimary (citable) accession number: Q96AK3
Secondary accession number(s): Q5JZ91
, Q7Z2N2, Q7Z2N5, Q7Z2N6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 29, 2004
Last sequence update: December 1, 2001
Last modified: September 12, 2018
This is version 127 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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Main funding by: National Institutes of Health

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