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Protein

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

Gene

APOBEC3H

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. The A3H-var/haplotype 2 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. Exhibits antiviral activity also against T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons.10 Publications

Catalytic activityi

Cytidine + H2O = uridine + NH3.

Cofactori

Zn2+By similarity

Enzyme 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 bindingi54ZincBy similarity1
Active sitei56Proton donorBy similarity1
Metal bindingi85ZincBy similarity1
Metal bindingi88ZincBy similarity1

GO - Molecular functioni

  • cytidine deaminase activity Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • defense response to virus Source: UniProtKB
  • DNA cytosine deamination Source: UniProtKB
  • innate immune response Source: UniProtKB-KW
  • negative regulation of single stranded viral RNA replication via double stranded DNA intermediate Source: UniProtKB
  • negative regulation of transposition Source: UniProtKB
  • negative regulation of viral process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Antiviral defense, Immunity, Innate immunity

Keywords - Ligandi

Metal-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-3H (EC:3.5.4.-)
Alternative name(s):
APOBEC-related protein 10
Short name:
ARP-10
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3H
Short name:
A3H
Gene namesi
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

HGNCiHGNC:24100. APOBEC3H.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytoplasmic mRNA processing body Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi56E → Q: Reduces the ability to inhibit the retrotransposition of LINE-1 elements. 1 Publication1

Organism-specific databases

DisGeNETi164668.
PharmGKBiPA162376694.

Polymorphism and mutation databases

BioMutaiAPOBEC3H.
DMDMi205371798.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002916631 – 200DNA dC->dU-editing enzyme APOBEC-3HAdd BLAST200

Proteomic databases

PaxDbiQ6NTF7.
PRIDEiQ6NTF7.

PTM databases

iPTMnetiQ6NTF7.
PhosphoSitePlusiQ6NTF7.

Expressioni

Tissue specificityi

Expressed in lymphoid organs. Also detected in non-lymphoid tissues including lung, testis, ovary, fetal liver and skin.2 Publications

Gene expression databases

BgeeiENSG00000100298.
CleanExiHS_APOBEC3H.
ExpressionAtlasiQ6NTF7. baseline and differential.

Organism-specific databases

HPAiHPA021492.

Interactioni

Subunit structurei

Interacts with AGO1, AGO2 and AGO3.1 Publication

Protein-protein interaction databases

BioGridi127899. 1 interactor.
STRINGi9606.ENSP00000385741.

Structurei

3D structure databases

ProteinModelPortaliQ6NTF7.
SMRiQ6NTF7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini4 – 126CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd BLAST123

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili160 – 182Sequence analysisAdd BLAST23

Sequence similaritiesi

Contains 1 CMP/dCMP-type deaminase domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG410JBA1. Eukaryota.
ENOG41119MS. LUCA.
HOGENOMiHOG000033754.
HOVERGENiHBG050434.
KOiK18750.
PhylomeDBiQ6NTF7.
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. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q6NTF7-1) [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
MALLTAETFR LQFNNKRRLR RPYYPRKALL CYQLTPQNGS TPTRGYFENK
60 70 80 90 100
KKCHAEICFI NEIKSMGLDE TQCYQVTCYL TWSPCSSCAW ELVDFIKAHD
110 120 130 140 150
HLNLGIFASR LYYHWCKPQQ KGLRLLCGSQ VPVEVMGFPK FADCWENFVD
160 170 180 190 200
HEKPLSFNPY KMLEELDKNS RAIKRRLERI KIPGVRAQGR YMDILCDAEV
Note: No experimental confirmation available.
Length:200
Mass (Da):23,531
Last modified:September 2, 2008 - v3
Checksum:i6F89E0138CC29386
GO
Isoform 2 (identifier: Q6NTF7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     182-200: IPGVRAQGRYMDILCDAEV → S

Show »
Length:182
Mass (Da):21,530
Checksum:i96BDB820405132F0
GO
Isoform 3 (identifier: Q6NTF7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     182-200: IPGVRAQGRYMDILCDAEV → QS

Show »
Length:183
Mass (Da):21,658
Checksum:iEC45DDB820405132
GO
Isoform 4 (identifier: Q6NTF7-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     140-200: KFADCWENFV...YMDILCDAEV → NSRGTCAGSLHGYIV

Note: Gene prediction based on EST data.
Show »
Length:154
Mass (Da):17,782
Checksum:i24B2D720CD100775
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti121K → D in CAG30367 (PubMed:15461802).Curated1

Polymorphismi

There are at least 4 different haplotypes in the human population. The allele A3H-var/haplotype 2 encodes a more stable protein which is able to block HIV-1 replication. The displayed allele (haplotype 1) is unstable and inefficient to block HIV-1 replication.

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_06562215Missing Decreases protein stability. 2 Publications1
Natural variantiVAR_03283518R → L.1 PublicationCorresponds to variant rs139293dbSNPEnsembl.1
Natural variantiVAR_032836105G → R in allele A3H-Var; haplotype 2; allele presenting a higher expression and which is more effective in retrotransposons and HIV-1 restriction; increases protein stability and exhibits a cytoplasmic localization. 2 PublicationsCorresponds to variant rs139297dbSNPEnsembl.1
Natural variantiVAR_032837121K → E in allele A3H-Var; haplotype 2; allele presenting a higher expression and more effective in retrotransposons and HIV-1 restriction. Corresponds to variant rs139298dbSNPEnsembl.1
Natural variantiVAR_032838121K → N.Corresponds to variant rs139299dbSNPEnsembl.1
Natural variantiVAR_067444140K → E.3 PublicationsCorresponds to variant rs139300dbSNPEnsembl.1
Natural variantiVAR_032839178E → D in allele A3H-Var; haplotype 2; allele presenting a higher expression and more effective in retrotransposons and HIV-1 restriction. 1 PublicationCorresponds to variant rs139302dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_047044140 – 200KFADC…CDAEV → NSRGTCAGSLHGYIV in isoform 4. CuratedAdd BLAST61
Alternative sequenceiVSP_035034182 – 200IPGVR…CDAEV → S in isoform 2. 2 PublicationsAdd BLAST19
Alternative sequenceiVSP_039975182 – 200IPGVR…CDAEV → QS in isoform 3. 1 PublicationAdd BLAST19

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ376613 mRNA. Translation: ACK77774.1.
CR456481 mRNA. Translation: CAG30367.3.
AL031846 Genomic DNA. No translation available.
BC069023 mRNA. Translation: AAH69023.1.
BQ052182 mRNA. No translation available.
CCDSiCCDS13985.1. [Q6NTF7-3]
CCDS54530.1. [Q6NTF7-1]
CCDS54531.1. [Q6NTF7-2]
CCDS54532.1. [Q6NTF7-4]
RefSeqiNP_001159474.2. NM_001166002.2.
NP_001159475.2. NM_001166003.2.
NP_001159476.2. NM_001166004.2.
NP_861438.3. NM_181773.4.
XP_011528294.1. XM_011529992.2.
UniGeneiHs.440515.

Genome annotation databases

EnsembliENST00000348946; ENSP00000216123; ENSG00000100298.
ENST00000401756; ENSP00000385741; ENSG00000100298.
ENST00000421988; ENSP00000393520; ENSG00000100298.
ENST00000442487; ENSP00000411754; ENSG00000100298.
GeneIDi164668.
KEGGihsa:164668.
UCSCiuc021wps.2. human. [Q6NTF7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ376613 mRNA. Translation: ACK77774.1.
CR456481 mRNA. Translation: CAG30367.3.
AL031846 Genomic DNA. No translation available.
BC069023 mRNA. Translation: AAH69023.1.
BQ052182 mRNA. No translation available.
CCDSiCCDS13985.1. [Q6NTF7-3]
CCDS54530.1. [Q6NTF7-1]
CCDS54531.1. [Q6NTF7-2]
CCDS54532.1. [Q6NTF7-4]
RefSeqiNP_001159474.2. NM_001166002.2.
NP_001159475.2. NM_001166003.2.
NP_001159476.2. NM_001166004.2.
NP_861438.3. NM_181773.4.
XP_011528294.1. XM_011529992.2.
UniGeneiHs.440515.

3D structure databases

ProteinModelPortaliQ6NTF7.
SMRiQ6NTF7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi127899. 1 interactor.
STRINGi9606.ENSP00000385741.

PTM databases

iPTMnetiQ6NTF7.
PhosphoSitePlusiQ6NTF7.

Polymorphism and mutation databases

BioMutaiAPOBEC3H.
DMDMi205371798.

Proteomic databases

PaxDbiQ6NTF7.
PRIDEiQ6NTF7.

Protocols and materials databases

DNASUi164668.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000348946; ENSP00000216123; ENSG00000100298.
ENST00000401756; ENSP00000385741; ENSG00000100298.
ENST00000421988; ENSP00000393520; ENSG00000100298.
ENST00000442487; ENSP00000411754; ENSG00000100298.
GeneIDi164668.
KEGGihsa:164668.
UCSCiuc021wps.2. human. [Q6NTF7-1]

Organism-specific databases

CTDi164668.
DisGeNETi164668.
GeneCardsiAPOBEC3H.
HGNCiHGNC:24100. APOBEC3H.
HPAiHPA021492.
MIMi610976. gene.
neXtProtiNX_Q6NTF7.
PharmGKBiPA162376694.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410JBA1. Eukaryota.
ENOG41119MS. LUCA.
HOGENOMiHOG000033754.
HOVERGENiHBG050434.
KOiK18750.
PhylomeDBiQ6NTF7.
TreeFamiTF331356.

Enzyme and pathway databases

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

Miscellaneous databases

GeneWikiiAPOBEC3H.
GenomeRNAii164668.
PROiQ6NTF7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000100298.
CleanExiHS_APOBEC3H.
ExpressionAtlasiQ6NTF7. baseline and differential.

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. 1 hit.
[Graphical view]
SUPFAMiSSF53927. SSF53927. 1 hit.
PROSITEiPS00903. CYT_DCMP_DEAMINASES_1. 1 hit.
PS51747. CYT_DCMP_DEAMINASES_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiABC3H_HUMAN
AccessioniPrimary (citable) accession number: Q6NTF7
Secondary accession number(s): B0QYP0
, B0QYP1, B7TQM5, E9PF38, Q5JYL9, Q6IC87
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: September 2, 2008
Last modified: November 30, 2016
This is version 106 of the entry and version 3 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

APOBEC3H from old world monkeys has retained its antiviral activity, while it is lost in other primates.
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

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. 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.