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Protein

5'-3' exoribonuclease 2

Gene

XRN2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Possesses 5'->3' exoribonuclease activity (By similarity). May promote the termination of transcription by RNA polymerase II. During transcription termination, cleavage at the polyadenylation site liberates a 5' fragment which is subsequently processed to form the mature mRNA and a 3' fragment which remains attached to the elongating polymerase. The processive degradation of this 3' fragment by this protein may promote termination of transcription. Binds to RNA polymerase II (RNAp II) transcription termination R-loops formed by G-rich pause sites (PubMed:21700224).By similarity3 Publications

Catalytic activityi

Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri262 – 278CCHC-typeAdd BLAST17

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: Reactome
  • 5'-3' exonuclease activity Source: UniProtKB
  • 5'-3' exoribonuclease activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • nuclease activity Source: ProtInc
  • poly(A) RNA binding Source: UniProtKB
  • transcription termination site sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  • cell growth Source: UniProtKB
  • DNA catabolic process, exonucleolytic Source: UniProtKB
  • DNA-templated transcription, termination Source: UniProtKB-KW
  • hippocampus development Source: Ensembl
  • mRNA processing Source: UniProtKB-KW
  • neuron differentiation Source: Ensembl
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • retina development in camera-type eye Source: Ensembl
  • RNA catabolic process Source: ProtInc
  • RNA metabolic process Source: UniProtKB
  • RNA processing Source: ProtInc
  • rRNA processing Source: Reactome
  • spermatogenesis Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, Transcription, Transcription regulation, Transcription termination

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000088930-MONOMER.
ReactomeiR-HSA-390471. Association of TriC/CCT with target proteins during biosynthesis.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Names & Taxonomyi

Protein namesi
Recommended name:
5'-3' exoribonuclease 2 (EC:3.1.13.-)
Alternative name(s):
DHM1-like protein
Short name:
DHP protein
Gene namesi
Name:XRN2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:12836. XRN2.

Subcellular locationi

GO - Cellular componenti

  • aggresome Source: HPA
  • membrane Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi22803.
OpenTargetsiENSG00000088930.
PharmGKBiPA37427.

Polymorphism and mutation databases

BioMutaiXRN2.
DMDMi30173484.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000713961 – 9505'-3' exoribonuclease 2Add BLAST950

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei286N6-acetyllysineBy similarity1
Modified residuei439PhosphothreonineCombined sources1
Modified residuei448PhosphoserineCombined sources1
Modified residuei471PhosphoserineCombined sources1
Modified residuei473PhosphoserineCombined sources1
Modified residuei475PhosphoserineCombined sources1
Modified residuei482PhosphoserineBy similarity1
Modified residuei487PhosphoserineCombined sources1
Modified residuei499PhosphoserineCombined sources1
Modified residuei501PhosphoserineCombined sources1
Modified residuei678PhosphoserineCombined sources1
Modified residuei824Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei824Omega-N-methylarginine; alternateCombined sources1
Modified residuei847Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei847Omega-N-methylarginine; alternateCombined sources1
Modified residuei851Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei851Omega-N-methylarginine; alternateCombined sources1
Modified residuei880Asymmetric dimethylarginineBy similarity1
Modified residuei883Asymmetric dimethylarginine; alternateBy similarity1
Modified residuei883Omega-N-methylarginine; alternateCombined sources1
Modified residuei895Omega-N-methylarginineCombined sources1
Modified residuei946Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei946Omega-N-methylarginine; alternateCombined sources1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

EPDiQ9H0D6.
MaxQBiQ9H0D6.
PaxDbiQ9H0D6.
PeptideAtlasiQ9H0D6.
PRIDEiQ9H0D6.

2D gel databases

SWISS-2DPAGEQ9H0D6.

PTM databases

iPTMnetiQ9H0D6.
PhosphoSitePlusiQ9H0D6.
SwissPalmiQ9H0D6.

Miscellaneous databases

PMAP-CutDBQ9H0D6.

Expressioni

Tissue specificityi

Expressed in the spleen, thymus, prostate, testis, ovary, small intestine, colon, peripheral blood leukocytes, heart, brain, placenta, lung, liver, skeletal muscle, kidney, and pancreas. Isoform 2 is expressed predominantly in peripheral blood leukocytes.2 Publications

Gene expression databases

BgeeiENSG00000088930.
CleanExiHS_XRN2.
GenevisibleiQ9H0D6. HS.

Organism-specific databases

HPAiHPA047118.
HPA050485.

Interactioni

Subunit structurei

Interacts with POLR2A and SMN1/SMN2 (PubMed:26700805). Interacts with CDKN2AIP and NKRF (PubMed:24462208). Interacts with CDKN2AIPNL; the interaction is direct (PubMed:26779609).3 Publications

Protein-protein interaction databases

BioGridi116483. 77 interactors.
DIPiDIP-31166N.
IntActiQ9H0D6. 38 interactors.
MINTiMINT-3065664.
STRINGi9606.ENSP00000366396.

Structurei

3D structure databases

ProteinModelPortaliQ9H0D6.
SMRiQ9H0D6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Contains 1 CCHC-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri262 – 278CCHC-typeAdd BLAST17

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG2044. Eukaryota.
COG5049. LUCA.
GeneTreeiENSGT00670000098098.
HOVERGENiHBG036677.
KOiK12619.
OMAiMGHESTE.
OrthoDBiEOG091G00A4.
PhylomeDBiQ9H0D6.
TreeFamiTF105977.

Family and domain databases

InterProiIPR027073. 5_3_exoribonuclease.
IPR017151. 5_3_exoribonuclease_2/3.
IPR004859. Put_53exo.
[Graphical view]
PANTHERiPTHR12341. PTHR12341. 1 hit.
PfamiPF03159. XRN_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037239. Exonuclease_Xrn2. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H0D6-1) [UniParc]FASTAAdd to basket
Also known as: XRN2a

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
MGVPAFFRWL SRKYPSIIVN CVEEKPKECN GVKIPVDASK PNPNDVEFDN
60 70 80 90 100
LYLDMNGIIH PCTHPEDKPA PKNEDEMMVA IFEYIDRLFS IVRPRRLLYM
110 120 130 140 150
AIDGVAPRAK MNQQRSRRFR ASKEGMEAAV EKQRVREEIL AKGGFLPPEE
160 170 180 190 200
IKERFDSNCI TPGTEFMDNL AKCLRYYIAD RLNNDPGWKN LTVILSDASA
210 220 230 240 250
PGEGEHKIMD YIRRQRAQPN HDPNTHHCLC GADADLIMLG LATHEPNFTI
260 270 280 290 300
IREEFKPNKP KPCGLCNQFG HEVKDCEGLP REKKGKHDEL ADSLPCAEGE
310 320 330 340 350
FIFLRLNVLR EYLERELTMA SLPFTFDVER SIDDWVFMCF FVGNDFLPHL
360 370 380 390 400
PSLEIRENAI DRLVNIYKNV VHKTGGYLTE SGYVNLQRVQ MIMLAVGEVE
410 420 430 440 450
DSIFKKRKDD EDSFRRRQKE KRKRMKRDQP AFTPSGILTP HALGSRNSPG
460 470 480 490 500
SQVASNPRQA AYEMRMQNNS SPSISPNTSF TSDGSPSPLG GIKRKAEDSD
510 520 530 540 550
SEPEPEDNVR LWEAGWKQRY YKNKFDVDAA DEKFRRKVVQ SYVEGLCWVL
560 570 580 590 600
RYYYQGCASW KWYYPFHYAP FASDFEGIAD MPSDFEKGTK PFKPLEQLMG
610 620 630 640 650
VFPAASGNFL PPSWRKLMSD PDSSIIDFYP EDFAIDLNGK KYAWQGVALL
660 670 680 690 700
PFVDERRLRA ALEEVYPDLT PEETRRNSLG GDVLFVGKHH PLHDFILELY
710 720 730 740 750
QTGSTEPVEV PPELCHGIQG KFSLDEEAIL PDQIVCSPVP MLRDLTQNTV
760 770 780 790 800
VSINFKDPQF AEDYIFKAVM LPGARKPAAV LKPSDWEKSS NGRQWKPQLG
810 820 830 840 850
FNRDRRPVHL DQAAFRTLGH VMPRGSGTGI YSNAAPPPVT YQGNLYRPLL
860 870 880 890 900
RGQAQIPKLM SNMRPQDSWR GPPPLFQQQR FDRGVGAEPL LPWNRMLQTQ
910 920 930 940 950
NAAFQPNQYQ MLAGPGGYPP RRDDRGGRQG YPREGRKYPL PPPSGRYNWN
Length:950
Mass (Da):108,582
Last modified:March 1, 2001 - v1
Checksum:i763B5E0E628F97A8
GO
Isoform 2 (identifier: Q9H0D6-2) [UniParc]FASTAAdd to basket
Also known as: XRN2b

The sequence of this isoform differs from the canonical sequence as follows:
     1-76: Missing.

Note: No experimental confirmation available.
Show »
Length:874
Mass (Da):99,962
Checksum:i85DBF4213F810AEC
GO

Sequence cautioni

The sequence AAR24369 differs from that shown. Reason: Frameshift at position 73.Curated
The sequence BAA90934 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti14Y → C in AAQ13577 (PubMed:10409438).Curated1
Sequence conflicti109A → V in AAD55138 (PubMed:10409438).Curated1
Sequence conflicti109A → V in AAQ13577 (PubMed:10409438).Curated1
Sequence conflicti122 – 124SKE → IKR in AAD55138 (PubMed:10409438).Curated3
Sequence conflicti240 – 245GLATHE → AFPHMN in AAQ13577 (PubMed:10409438).Curated6
Sequence conflicti259K → R in AAD55138 (PubMed:10409438).Curated1
Sequence conflicti259K → R in AAQ13577 (PubMed:10409438).Curated1
Sequence conflicti280P → S in AAD55138 (PubMed:10409438).Curated1
Sequence conflicti280P → S in AAQ13577 (PubMed:10409438).Curated1
Sequence conflicti313L → V in AAQ13577 (PubMed:10409438).Curated1
Sequence conflicti463E → D in AAD55138 (PubMed:10409438).Curated1
Sequence conflicti582P → S in AAQ13577 (PubMed:10409438).Curated1
Sequence conflicti584D → E in AAD55138 (PubMed:10409438).Curated1
Sequence conflicti737S → A in AAD55138 (PubMed:10409438).Curated1
Sequence conflicti760F → L in AAR24369 (PubMed:16147866).Curated1
Sequence conflicti787E → G in AAD55138 (PubMed:10409438).Curated1
Sequence conflicti874P → L in AAR24369 (PubMed:16147866).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_027516743R → M.Corresponds to variant rs6137324dbSNPEnsembl.1
Natural variantiVAR_053002925R → C.Corresponds to variant rs6047420dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0205961 – 76Missing in isoform 2. 1 PublicationAdd BLAST76

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF064257 mRNA. Translation: AAD55138.1.
AF152169 mRNA. Translation: AAQ13577.1.
AY382900 mRNA. Translation: AAR24369.1. Frameshift.
AL136841 mRNA. Translation: CAB66775.1.
AL117332, AL158013 Genomic DNA. Translation: CAI19756.1.
AL158013, AL117332 Genomic DNA. Translation: CAH71495.1.
AK000084 mRNA. Translation: BAA90934.1. Different initiation.
BC006417 mRNA. Translation: AAH06417.2.
CCDSiCCDS13144.1. [Q9H0D6-1]
RefSeqiNP_001304889.1. NM_001317960.1.
NP_036387.2. NM_012255.4. [Q9H0D6-1]
UniGeneiHs.255932.

Genome annotation databases

EnsembliENST00000377191; ENSP00000366396; ENSG00000088930. [Q9H0D6-1]
GeneIDi22803.
KEGGihsa:22803.
UCSCiuc002wsf.2. human. [Q9H0D6-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF064257 mRNA. Translation: AAD55138.1.
AF152169 mRNA. Translation: AAQ13577.1.
AY382900 mRNA. Translation: AAR24369.1. Frameshift.
AL136841 mRNA. Translation: CAB66775.1.
AL117332, AL158013 Genomic DNA. Translation: CAI19756.1.
AL158013, AL117332 Genomic DNA. Translation: CAH71495.1.
AK000084 mRNA. Translation: BAA90934.1. Different initiation.
BC006417 mRNA. Translation: AAH06417.2.
CCDSiCCDS13144.1. [Q9H0D6-1]
RefSeqiNP_001304889.1. NM_001317960.1.
NP_036387.2. NM_012255.4. [Q9H0D6-1]
UniGeneiHs.255932.

3D structure databases

ProteinModelPortaliQ9H0D6.
SMRiQ9H0D6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116483. 77 interactors.
DIPiDIP-31166N.
IntActiQ9H0D6. 38 interactors.
MINTiMINT-3065664.
STRINGi9606.ENSP00000366396.

PTM databases

iPTMnetiQ9H0D6.
PhosphoSitePlusiQ9H0D6.
SwissPalmiQ9H0D6.

Polymorphism and mutation databases

BioMutaiXRN2.
DMDMi30173484.

2D gel databases

SWISS-2DPAGEQ9H0D6.

Proteomic databases

EPDiQ9H0D6.
MaxQBiQ9H0D6.
PaxDbiQ9H0D6.
PeptideAtlasiQ9H0D6.
PRIDEiQ9H0D6.

Protocols and materials databases

DNASUi22803.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000377191; ENSP00000366396; ENSG00000088930. [Q9H0D6-1]
GeneIDi22803.
KEGGihsa:22803.
UCSCiuc002wsf.2. human. [Q9H0D6-1]

Organism-specific databases

CTDi22803.
DisGeNETi22803.
GeneCardsiXRN2.
HGNCiHGNC:12836. XRN2.
HPAiHPA047118.
HPA050485.
MIMi608851. gene.
neXtProtiNX_Q9H0D6.
OpenTargetsiENSG00000088930.
PharmGKBiPA37427.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2044. Eukaryota.
COG5049. LUCA.
GeneTreeiENSGT00670000098098.
HOVERGENiHBG036677.
KOiK12619.
OMAiMGHESTE.
OrthoDBiEOG091G00A4.
PhylomeDBiQ9H0D6.
TreeFamiTF105977.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000088930-MONOMER.
ReactomeiR-HSA-390471. Association of TriC/CCT with target proteins during biosynthesis.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

ChiTaRSiXRN2. human.
GeneWikii5%27-3%27_exoribonuclease_2.
GenomeRNAii22803.
PMAP-CutDBQ9H0D6.
PROiQ9H0D6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000088930.
CleanExiHS_XRN2.
GenevisibleiQ9H0D6. HS.

Family and domain databases

InterProiIPR027073. 5_3_exoribonuclease.
IPR017151. 5_3_exoribonuclease_2/3.
IPR004859. Put_53exo.
[Graphical view]
PANTHERiPTHR12341. PTHR12341. 1 hit.
PfamiPF03159. XRN_N. 1 hit.
[Graphical view]
PIRSFiPIRSF037239. Exonuclease_Xrn2. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiXRN2_HUMAN
AccessioniPrimary (citable) accession number: Q9H0D6
Secondary accession number(s): Q3L8N4
, Q6KGZ9, Q9BQL1, Q9NTW0, Q9NXS6, Q9UL53
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: March 1, 2001
Last modified: November 30, 2016
This is version 150 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: 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.