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Protein

3'-5' exoribonuclease 1

Gene

ERI1

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

Functioni

RNA exonuclease that binds to the 3'-end of histone mRNAs and degrades them, suggesting that it plays an essential role in histone mRNA decay after replication. A 2' and 3'-hydroxyl groups at the last nucleotide of the histone 3'-end is required for efficient degradation of RNA substrates. Also able to degrade the 3'-overhangs of short interfering RNAs (siRNAs) in vitro, suggesting a possible role as regulator of RNA interference (RNAi). Requires for binding the 5'-ACCCA-3' sequence present in stem-loop structure. Able to bind other mRNAs. Required for 5.8S rRNA 3'-end processing. Also binds to 5.8s ribosomal RNA. Binds with high affinity to the stem-loop structure of replication-dependent histone pre-mRNAs.2 Publications

Cofactori

Mg2+Note: Binds 2 magnesium ions per subunit.

Enzyme regulationi

Although it can bind simultaneously with SLBP to the 3'-end of histone mRNA, the presence of SLBP prevents the exonuclease activity.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi134Magnesium 11
Metal bindingi134Magnesium 21
Active sitei136Proton acceptorSequence analysis1
Metal bindingi136Magnesium 11
Binding sitei136AMP1 Publication1
Binding sitei137AMP; via amide nitrogen and carbonyl oxygen1 Publication1
Metal bindingi234Magnesium 21
Active sitei293Proton acceptorSequence analysis1
Binding sitei293AMP1 Publication1
Metal bindingi298Magnesium 11

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease, RNA-binding
Biological processRNA-mediated gene silencing, rRNA processing
LigandMagnesium, Metal-binding

Enzyme and pathway databases

ReactomeiR-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Names & Taxonomyi

Protein namesi
Recommended name:
3'-5' exoribonuclease 1 (EC:3.1.-.-)
Alternative name(s):
3'-5' exonuclease ERI1
Eri-1 homolog
Histone mRNA 3'-end-specific exoribonuclease
Histone mRNA 3'-exonuclease 1
Protein 3'hExo
Short name:
HEXO
Gene namesi
Name:ERI1
Synonyms:3'EXO, THEX1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 8

Organism-specific databases

EuPathDBiHostDB:ENSG00000104626.14
HGNCiHGNC:23994 ERI1
MIMi608739 gene
neXtProtiNX_Q8IV48

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

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi92K → A: Does not inhibit RNA-binding to the stem-loop structure. Does not inhibit RNA-binding to the stem-loop structure, when associated with A-104. 1 Publication1
Mutagenesisi96R → A: Does not inhibit RNA-binding to the stem-loop structure. 1 Publication1
Mutagenesisi99K → A: Reduces slightly RNA-binding to the stem-loop structure. 1 Publication1
Mutagenesisi104K → A: Does not inhibit RNA-binding to the stem-loop structure. Does not inhibit RNA-binding to the stem-loop structure, when associated with A-92. 1 Publication1
Mutagenesisi105R → A: Inhibits RNA-binding to the stem-loop structure. 1 Publication1
Mutagenesisi109Y → A: Reduces slightly RNA-binding to the stem-loop structure; when associated with A-110. 1 Publication1
Mutagenesisi110Y → A: Reduces slightly RNA-binding to the stem-loop structure; when associated with A-109. 1 Publication1
Mutagenesisi111K → A: Reduces RNA-binding to the stem-loop structure but not 3'-end histone mRNA exonuclease activity; when associated with A-112. 1 Publication1
Mutagenesisi112K → A: Reduces RNA-binding to the stem-loop structure but not 3'-end histone mRNA exonuclease activity; when associated with A-111. 1 Publication1
Mutagenesisi234D → A: Inhibits 3'-end histone mRNA exonuclease activity. 1 Publication1
Mutagenesisi235M → A: Inhibits RNA-binding to the stem-loop structure and 3'-end histone mRNA exonuclease activity. 1 Publication1
Mutagenesisi298D → A: Inhibits 3'-end histone mRNA exonuclease activity. 1 Publication1

Organism-specific databases

DisGeNETi90459
OpenTargetsiENSG00000104626
PharmGKBiPA164719226

Polymorphism and mutation databases

BioMutaiERI1
DMDMi45476938

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001870072 – 3493'-5' exoribonuclease 1Add BLAST348

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei59PhosphoserineCombined sources1
Modified residuei62PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8IV48
MaxQBiQ8IV48
PaxDbiQ8IV48
PeptideAtlasiQ8IV48
PRIDEiQ8IV48
ProteomicsDBi70659

PTM databases

iPTMnetiQ8IV48
PhosphoSitePlusiQ8IV48

Expressioni

Gene expression databases

BgeeiENSG00000104626
CleanExiHS_ERI1
ExpressionAtlasiQ8IV48 baseline and differential
GenevisibleiQ8IV48 HS

Organism-specific databases

HPAiCAB033838
HPA055548
HPA056074

Interactioni

Subunit structurei

Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1. Interacts in a cooperative manner with SLBP to the mature 3'-end of histone mRNAs (By similarity). Binds to 40S and 60S ribosomal subunits and to 80S assembled ribosomes. Found in a ternary complex with SLBP and the stem-loop structure of the 3'-end of histone mRNAs.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SLBPQ144932EBI-5459222,EBI-2696402

Protein-protein interaction databases

BioGridi124718, 16 interactors
DIPiDIP-61409N
IntActiQ8IV48, 12 interactors
STRINGi9606.ENSP00000250263

Structurei

Secondary structure

1349
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi47 – 49Combined sources3
Turni50 – 52Combined sources3
Beta strandi53 – 57Combined sources5
Helixi64 – 77Combined sources14
Helixi81 – 90Combined sources10
Helixi99 – 114Combined sources16
Beta strandi115 – 119Combined sources5
Beta strandi126 – 132Combined sources7
Beta strandi151 – 160Combined sources10
Turni161 – 163Combined sources3
Beta strandi165 – 174Combined sources10
Beta strandi177 – 179Combined sources3
Helixi184 – 190Combined sources7
Helixi194 – 198Combined sources5
Beta strandi200 – 202Combined sources3
Helixi203 – 216Combined sources14
Turni220 – 222Combined sources3
Beta strandi225 – 231Combined sources7
Turni232 – 235Combined sources4
Helixi236 – 246Combined sources11
Helixi252 – 254Combined sources3
Beta strandi255 – 259Combined sources5
Helixi260 – 268Combined sources9
Helixi272 – 274Combined sources3
Helixi277 – 283Combined sources7
Helixi295 – 311Combined sources17
Beta strandi320 – 323Combined sources4
Beta strandi326 – 329Combined sources4
Beta strandi332 – 334Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1W0HX-ray1.59A123-322[»]
1ZBHX-ray3.00A/B/C/D51-349[»]
1ZBUX-ray3.00A/B/C/D1-349[»]
4L8RX-ray2.60B/E55-349[»]
4QOZX-ray2.30B/E55-349[»]
ProteinModelPortaliQ8IV48
SMRiQ8IV48
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8IV48

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini76 – 110SAPPROSITE-ProRule annotationAdd BLAST35
Domaini130 – 306ExonucleaseAdd BLAST177

Domaini

The SAP domain is necessary for binding to the stem-loop structure of histone mRNAs and to form the ternary complex with SLBP, but not for 3'-end histone mRNA exonuclease activity.

Phylogenomic databases

eggNOGiKOG0542 Eukaryota
COG5018 LUCA
GeneTreeiENSGT00530000063205
HOGENOMiHOG000006635
HOVERGENiHBG048925
KOiK18416
OMAiTKYKYCI
OrthoDBiEOG091G0ISP
PhylomeDBiQ8IV48
TreeFamiTF313449

Family and domain databases

Gene3Di1.10.720.30, 1 hit
3.30.420.10, 1 hit
InterProiView protein in InterPro
IPR013520 Exonuclease_RNaseT/DNA_pol3
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
IPR003034 SAP_dom
IPR036361 SAP_dom_sf
PfamiView protein in Pfam
PF00929 RNase_T, 1 hit
PF02037 SAP, 1 hit
SMARTiView protein in SMART
SM00479 EXOIII, 1 hit
SM00513 SAP, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
SSF68906 SSF68906, 1 hit
PROSITEiView protein in PROSITE
PS50800 SAP, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q8IV48-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEDPQSKEPA GEAVALALLE SPRPEGGEEP PRPSPEETQQ CKFDGQETKG
60 70 80 90 100
SKFITSSASD FSDPVYKEIA ITNGCINRMS KEELRAKLSE FKLETRGVKD
110 120 130 140 150
VLKKRLKNYY KKQKLMLKES NFADSYYDYI CIIDFEATCE EGNPPEFVHE
160 170 180 190 200
IIEFPVVLLN THTLEIEDTF QQYVRPEINT QLSDFCISLT GITQDQVDRA
210 220 230 240 250
DTFPQVLKKV IDWMKLKELG TKYKYSLLTD GSWDMSKFLN IQCQLSRLKY
260 270 280 290 300
PPFAKKWINI RKSYGNFYKV PRSQTKLTIM LEKLGMDYDG RPHCGLDDSK
310 320 330 340
NIARIAVRML QDGCELRINE KMHAGQLMSV SSSLPIEGTP PPQMPHFRK
Length:349
Mass (Da):40,064
Last modified:January 23, 2007 - v3
Checksum:iD5837AA05F09410C
GO

Sequence cautioni

The sequence CAB70871 differs from that shown. Reason: Frameshift at position 117.Curated
The sequence CAB70871 differs from that shown. Reason: Erroneous termination at position 159. Translated as Leu.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01810716L → P1 PublicationCorresponds to variant dbSNP:rs2288672Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY310909 mRNA Translation: AAQ21219.1
AK291062 mRNA Translation: BAF83751.1
AL137679 mRNA Translation: CAB70871.2 Sequence problems.
BC035279 mRNA Translation: AAH35279.1
CCDSiCCDS5972.1
PIRiT46432
RefSeqiNP_699163.2, NM_153332.3
UniGeneiHs.20000

Genome annotation databases

EnsembliENST00000250263; ENSP00000250263; ENSG00000104626
ENST00000519292; ENSP00000430190; ENSG00000104626
ENST00000523898; ENSP00000429615; ENSG00000104626
GeneIDi90459
KEGGihsa:90459
UCSCiuc003wsk.2 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiERI1_HUMAN
AccessioniPrimary (citable) accession number: Q8IV48
Secondary accession number(s): A8K4U7, Q9NSX3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: January 23, 2007
Last modified: June 20, 2018
This is version 158 of the entry and version 3 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 8
    Human chromosome 8: 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

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