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Protein

5'-3' exoribonuclease 2

Gene

Xrn2

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Possesses 5'->3' exoribonuclease activity. 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 (By similarity).By similarity

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

  • cell growth Source: UniProtKB
  • DNA catabolic process, exonucleolytic Source: UniProtKB
  • DNA recombination Source: UniProtKB
  • DNA repair Source: UniProtKB
  • DNA-templated transcription, termination Source: UniProtKB-KW
  • hippocampus development Source: Ensembl
  • microtubule-based process Source: UniProtKB
  • 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 metabolic process Source: UniProtKB
  • 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

ReactomeiR-MMU-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):
Protein Dhm1
Gene namesi
Name:Xrn2
Synonyms:Dhm1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 2

Organism-specific databases

MGIiMGI:894687. Xrn2.

Subcellular locationi

GO - Cellular componenti

  • aggresome Source: MGI
  • membrane Source: MGI
  • nucleolus Source: UniProtKB
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000713971 – 9515'-3' exoribonuclease 2Add BLAST951

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei286N6-acetyllysineCombined sources1
Modified residuei439PhosphothreonineBy similarity1
Modified residuei448PhosphoserineCombined sources1
Modified residuei471PhosphoserineCombined sources1
Modified residuei473PhosphoserineBy similarity1
Modified residuei475PhosphoserineCombined sources1
Modified residuei482PhosphoserineCombined sources1
Modified residuei487PhosphoserineCombined sources1
Modified residuei499PhosphoserineCombined sources1
Modified residuei501PhosphoserineCombined sources1
Modified residuei678PhosphoserineCombined sources1
Modified residuei824Asymmetric dimethylarginine; alternateBy similarity1
Modified residuei824Omega-N-methylarginine; alternateBy similarity1
Modified residuei847Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei847Omega-N-methylarginine; alternateBy similarity1
Modified residuei851Asymmetric dimethylarginine; alternateBy similarity1
Modified residuei851Omega-N-methylarginine; alternateBy similarity1
Modified residuei880Asymmetric dimethylarginineCombined sources1
Modified residuei883Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei883Omega-N-methylarginine; alternateBy similarity1
Modified residuei895Omega-N-methylarginineCombined sources1
Modified residuei947Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei947Omega-N-methylarginine; alternateBy similarity1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ9DBR1.
PeptideAtlasiQ9DBR1.
PRIDEiQ9DBR1.

PTM databases

iPTMnetiQ9DBR1.
PhosphoSitePlusiQ9DBR1.

Expressioni

Tissue specificityi

Expressed in the spleen, testis, heart, brain, lung, liver, skeletal muscle, and kidney.1 Publication

Gene expression databases

BgeeiENSMUSG00000027433.
CleanExiMM_XRN2.
GenevisibleiQ9DBR1. MM.

Interactioni

Subunit structurei

Interacts with POLR2A and SMN1/SMN2. Interacts with CDKN2AIP and NKRF. Interacts with CDKN2AIPNL; the interaction is direct.By similarity

Protein-protein interaction databases

BioGridi204910. 2 interactors.
IntActiQ9DBR1. 4 interactors.
MINTiMINT-4140454.
STRINGi10090.ENSMUSP00000028921.

Structurei

3D structure databases

ProteinModelPortaliQ9DBR1.
SMRiQ9DBR1.
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.
HOGENOMiHOG000205514.
HOVERGENiHBG036677.
InParanoidiQ9DBR1.
KOiK12619.
OMAiPTWRKLM.
OrthoDBiEOG091G00A4.
PhylomeDBiQ9DBR1.
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: Q9DBR1-1) [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
MGVPAFFRWL SRKYPSIIVN CVEEKPKECN GVKIPVDASK PNPNDVEFDN
60 70 80 90 100
LYLDMNGIIH PCTHPEDKPA PKNEDEMMVA IFEYIDRLFN 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 KPCALCNQFG HEVKDCEGLP REKKGKHDEL ADSLPCAEGE
310 320 330 340 350
FIFLRLNVLR EYLERELTMA SLPFPFDVER SIDDWVFMCF FVGNDFLPHL
360 370 380 390 400
PSLEIREGAI DRLVNIYKNV VHKTGGYLTE SGYVNLQRVQ MIMLAVGEVE
410 420 430 440 450
DSIFKKRKDD EDSFRRRQKE KRKRMKRDQP AFTPSGILTP HALGSRNSPG
460 470 480 490 500
CQVASNPRQA AYEMRMQRNS SPSISPNTSF ASDGSPSPLG GIKRKAEDSD
510 520 530 540 550
SEPEPEDNVR LWEAGWKQRY YKNKFDVDAA DEKFRRKVVQ SYVEGLCWVL
560 570 580 590 600
RYYYQGCASW KWYYPFHYAP FASDFEGIAD MSSEFEKGTK PFKPLEQLMG
610 620 630 640 650
VFPAASGNFL PPTWRKLMSD PDSSIIDFYP EDFAIDLNGK KYAWQGVALL
660 670 680 690 700
PFVDERRLRA ALEEVYPDLT PEENRRNSLG GDVLFVGKLH PLRDFILELY
710 720 730 740 750
QTGSTEPVDV PPELCHGIQG TFSLDEEAIL PDQTVCSPVP MLRDLTQNTA
760 770 780 790 800
VSINFKDPQF AEDYVFKAAM LPGARKPATV LKPGDWEKSS NGRQWKPQLG
810 820 830 840 850
FNRDRRPVHL DQAAFRTLGH VTPRGSGTSV YTNTALPPAN YQGNNYRPLL
860 870 880 890 900
RGQAQIPKLM SNMRPQDSWR GPPPLFQQHR FERSVGAEPL LPWNRMIQNQ
910 920 930 940 950
NAAFQPNQYQ MLGGPGGYPP RRDDHRGGRQ GYPREGRKYP LPPPSGRYSW

N
Length:951
Mass (Da):108,687
Last modified:June 1, 2001 - v1
Checksum:iCF57479291DD18B9
GO
Isoform 2 (identifier: Q9DBR1-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     931-951: GYPREGRKYPLPPPSGRYSWN → VISTMWAVEGKQHTAHC

Note: No experimental confirmation available. May result from the retention of an intron in the cDNA.
Show »
Length:947
Mass (Da):108,108
Checksum:iD07EDE545BB57F24
GO

Sequence cautioni

The sequence AAH04028 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti122 – 124SKE → IKG in BAA07524 (PubMed:7885830).Curated3
Sequence conflicti221H → Q in BAA07524 (PubMed:7885830).Curated1
Sequence conflicti306L → P in BAE40020 (PubMed:16141072).Curated1
Sequence conflicti332I → N in BAA07524 (PubMed:7885830).Curated1
Sequence conflicti336V → E in BAA07524 (PubMed:7885830).Curated1
Sequence conflicti440P → H in BAE40020 (PubMed:16141072).Curated1
Sequence conflicti449P → Q in BAE40020 (PubMed:16141072).Curated1
Sequence conflicti493K → R in BAA07524 (PubMed:7885830).Curated1
Sequence conflicti563Y → L in BAA07524 (PubMed:7885830).Curated1
Sequence conflicti712P → H in BAC27318 (PubMed:16141072).Curated1
Sequence conflicti734T → K in BAC27318 (PubMed:16141072).Curated1
Sequence conflicti837P → L in BAA07524 (PubMed:7885830).Curated1
Sequence conflicti866Q → K in BAA07524 (PubMed:7885830).Curated1
Sequence conflicti889P → H in BAC27318 (PubMed:16141072).Curated1
Sequence conflicti923D → G in BAE40020 (PubMed:16141072).Curated1
Sequence conflicti930Q → QV in BAC27318 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_007235931 – 951GYPRE…RYSWN → VISTMWAVEGKQHTAHC in isoform 2. 1 PublicationAdd BLAST21

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D38517 mRNA. Translation: BAA07524.1.
AK004800 mRNA. Translation: BAB23573.1.
AK031247 mRNA. Translation: BAC27318.1.
AK053643 mRNA. Translation: BAC35458.1.
AK133654 mRNA. Translation: BAE21766.1.
AK167019 mRNA. Translation: BAE39193.1.
AK168037 mRNA. Translation: BAE40020.1.
BC004028 mRNA. Translation: AAH04028.1. Different initiation.
BC054743 mRNA. Translation: AAH54743.1.
CCDSiCCDS38258.1. [Q9DBR1-1]
PIRiI49635.
RefSeqiNP_036047.2. NM_011917.2. [Q9DBR1-1]
UniGeneiMm.3065.

Genome annotation databases

EnsembliENSMUST00000028921; ENSMUSP00000028921; ENSMUSG00000027433. [Q9DBR1-1]
GeneIDi24128.
KEGGimmu:24128.
UCSCiuc008msq.1. mouse. [Q9DBR1-2]
uc008msr.1. mouse. [Q9DBR1-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D38517 mRNA. Translation: BAA07524.1.
AK004800 mRNA. Translation: BAB23573.1.
AK031247 mRNA. Translation: BAC27318.1.
AK053643 mRNA. Translation: BAC35458.1.
AK133654 mRNA. Translation: BAE21766.1.
AK167019 mRNA. Translation: BAE39193.1.
AK168037 mRNA. Translation: BAE40020.1.
BC004028 mRNA. Translation: AAH04028.1. Different initiation.
BC054743 mRNA. Translation: AAH54743.1.
CCDSiCCDS38258.1. [Q9DBR1-1]
PIRiI49635.
RefSeqiNP_036047.2. NM_011917.2. [Q9DBR1-1]
UniGeneiMm.3065.

3D structure databases

ProteinModelPortaliQ9DBR1.
SMRiQ9DBR1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi204910. 2 interactors.
IntActiQ9DBR1. 4 interactors.
MINTiMINT-4140454.
STRINGi10090.ENSMUSP00000028921.

PTM databases

iPTMnetiQ9DBR1.
PhosphoSitePlusiQ9DBR1.

Proteomic databases

PaxDbiQ9DBR1.
PeptideAtlasiQ9DBR1.
PRIDEiQ9DBR1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000028921; ENSMUSP00000028921; ENSMUSG00000027433. [Q9DBR1-1]
GeneIDi24128.
KEGGimmu:24128.
UCSCiuc008msq.1. mouse. [Q9DBR1-2]
uc008msr.1. mouse. [Q9DBR1-1]

Organism-specific databases

CTDi22803.
MGIiMGI:894687. Xrn2.

Phylogenomic databases

eggNOGiKOG2044. Eukaryota.
COG5049. LUCA.
GeneTreeiENSGT00670000098098.
HOGENOMiHOG000205514.
HOVERGENiHBG036677.
InParanoidiQ9DBR1.
KOiK12619.
OMAiPTWRKLM.
OrthoDBiEOG091G00A4.
PhylomeDBiQ9DBR1.
TreeFamiTF105977.

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiXrn2. mouse.
PROiQ9DBR1.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000027433.
CleanExiMM_XRN2.
GenevisibleiQ9DBR1. MM.

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_MOUSE
AccessioniPrimary (citable) accession number: Q9DBR1
Secondary accession number(s): Q3TI26
, Q3TKF2, Q3UZT9, Q61489, Q99KS7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: June 1, 2001
Last modified: November 2, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.