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Protein

5'-3' exoribonuclease 2

Gene

XRN2

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

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Exonuclease, Hydrolase, Nuclease
Biological processmRNA processing, Transcription, Transcription regulation, Transcription termination
LigandMetal-binding, Zinc

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000088930.7
HGNCiHGNC:12836 XRN2
MIMi608851 gene
neXtProtiNX_Q9H0D6

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

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
ProteomicsDBi80258
80259 [Q9H0D6-2]

2D gel databases

SWISS-2DPAGEiQ9H0D6

PTM databases

iPTMnetiQ9H0D6
PhosphoSitePlusiQ9H0D6
SwissPalmiQ9H0D6

Miscellaneous databases

PMAP-CutDBiQ9H0D6

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 Expressed in 192 organ(s), highest expression level in kidney
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). Interacts with TRIM71 (via NHL repeats) in an RNA-dependent manner (PubMed:23125361).4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CDKN2AIPNLQ96HQ22EBI-372110,EBI-10038935

Protein-protein interaction databases

BioGridi116483, 83 interactors
CORUMiQ9H0D6
DIPiDIP-31166N
IntActiQ9H0D6, 48 interactors
MINTiQ9H0D6
STRINGi9606.ENSP00000366396

Structurei

3D structure databases

ProteinModelPortaliQ9H0D6
SMRiQ9H0D6
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

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
OMAiGEHFDSN
OrthoDBiEOG091G00A4
PhylomeDBiQ9H0D6
TreeFamiTF105977

Family and domain databases

InterProiView protein in InterPro
IPR027073 5_3_exoribonuclease
IPR004859 Put_53exo
IPR017151 Xrn2/3/4
PANTHERiPTHR12341 PTHR12341, 1 hit
PfamiView protein in Pfam
PF03159 XRN_N, 1 hit
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. Translation N-terminally extended.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 dbSNP:rs6137324Ensembl.1
Natural variantiVAR_053002925R → C. Corresponds to variant dbSNP:rs6047420Ensembl.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 Genomic DNA No translation available.
AL158013 Genomic DNA No translation available.
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

Similar proteinsi

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 Genomic DNA No translation available.
AL158013 Genomic DNA No translation available.
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, 83 interactors
CORUMiQ9H0D6
DIPiDIP-31166N
IntActiQ9H0D6, 48 interactors
MINTiQ9H0D6
STRINGi9606.ENSP00000366396

PTM databases

iPTMnetiQ9H0D6
PhosphoSitePlusiQ9H0D6
SwissPalmiQ9H0D6

Polymorphism and mutation databases

BioMutaiXRN2
DMDMi30173484

2D gel databases

SWISS-2DPAGEiQ9H0D6

Proteomic databases

EPDiQ9H0D6
MaxQBiQ9H0D6
PaxDbiQ9H0D6
PeptideAtlasiQ9H0D6
PRIDEiQ9H0D6
ProteomicsDBi80258
80259 [Q9H0D6-2]

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
EuPathDBiHostDB:ENSG00000088930.7
GeneCardsiXRN2
HGNCiHGNC:12836 XRN2
HPAiHPA047118
HPA050485
MIMi608851 gene
neXtProtiNX_Q9H0D6
OpenTargetsiENSG00000088930
PharmGKBiPA37427
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2044 Eukaryota
COG5049 LUCA
GeneTreeiENSGT00670000098098
HOVERGENiHBG036677
KOiK12619
OMAiGEHFDSN
OrthoDBiEOG091G00A4
PhylomeDBiQ9H0D6
TreeFamiTF105977

Enzyme and pathway databases

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-CutDBiQ9H0D6
PROiPR:Q9H0D6
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000088930 Expressed in 192 organ(s), highest expression level in kidney
CleanExiHS_XRN2
GenevisibleiQ9H0D6 HS

Family and domain databases

InterProiView protein in InterPro
IPR027073 5_3_exoribonuclease
IPR004859 Put_53exo
IPR017151 Xrn2/3/4
PANTHERiPTHR12341 PTHR12341, 1 hit
PfamiView protein in Pfam
PF03159 XRN_N, 1 hit
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 historyiIntegrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: March 1, 2001
Last modified: October 10, 2018
This is version 165 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 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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