Exosome complex exonuclease RRP41 - Homo sapiens (Human)

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Reviewed, UniProtKB/Swiss-Prot Q9NPD3 (EXOS4_HUMAN)

Last modified June 16, 2009. Version 81. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Exosome complex exonuclease RRP41
    EC=3.1.13.-
Alternative name(s):
    Ribosomal RNA-processing protein 41
    Exosome component 4
    p12A

Gene names

Name:	EXOSC4
Synonyms:	RRP41, SKI6

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length	245 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Component of the exosome 3'->5' exoribonuclease complex, a complex that degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3'-untranslated regions. Required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA. Has a 3'-5' exonuclease activity.
Subunit structure	Component of the exosome multienzyme ribonuclease complex composed of at least 11 proteins: EXOSC1/CSL4, EXOSC2/RRP4, EXOSC3/RRP40, EXOSC4/RRP41, EXOSC5/RRP46, EXOSC6/MTR3, EXOSC7/RRP42, EXOSC8/RRP43, EXOSC9/Scl-75, DIS3/RRP44, and EXOSC10/Scl-100 (only in the nuclear complex). Found in a mRNA decay complex with RENT1, RENT2 and RENT3B. Also associated with the GTPase Ran.
Subcellular location	Cytoplasm. Nucleus › nucleolus.
Sequence similarities	Belongs to the RNase PH family.

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Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm Exosome Nucleus
Ligand	RNA-binding
Molecular function	Exonuclease Hydrolase Nuclease
PTM	Acetylation
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	rRNA processing Ref.1 Non-traceable author statement. Source: UniProtKB
Cellular component	cytoplasm Ref.1 Non-traceable author statement. Source: UniProtKB exosome (RNase complex) Inferred from electronic annotation. Source: UniProtKB-KW nucleolus Ref.1 Non-traceable author statement. Source: UniProtKB
Molecular function	3'-5'-exoribonuclease activity Ref.1 Non-traceable author statement. Source: UniProtKB RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
AKR1A1	P14550	1	EBI-371823,EBI-372388
DOM3Z	O77932	1	EBI-371823,EBI-372173
EEF1A1	P68104	1	EBI-371823,EBI-352162
EXOSC1	Q9Y3B2	2	EBI-371823,EBI-371892
EXOSC10	Q01780	1	EBI-371823,EBI-358236
EXOSC3	Q9NQT5	1	EBI-371823,EBI-371866
EXOSC9	Q06265	1	EBI-371823,EBI-347966
FAHD1	Q6P587	1	EBI-371823,EBI-597013
GADD45GIP1	Q8TAE8	1	EBI-371823,EBI-372506
GTF2IRD1	Q9UHL9	1	EBI-371823,EBI-372530
HNRNPD	Q14103-3	1	EBI-371823,EBI-432539
LRRC8D	Q7L1W4	1	EBI-371823,EBI-861997
MPZL1	Q8WUP4	1	EBI-371823,EBI-372210
NEK1	Q96PY6	1	EBI-371823,EBI-373615
SKIV2L	Q15477	1	EBI-371823,EBI-373226
SMPD4	Q9NXE4	1	EBI-371823,EBI-372102
TSEN15	Q8WW01	1	EBI-371823,EBI-372432

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.4

Chain

2 – 245

244

Exosome complex exonuclease RRP41

PRO_0000139958

Amino acid modifications

Modified residue

N-acetylalanine Ref.4

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Sequences

Sequence

Length

Mass (Da)

Tools

Q9NPD3-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 7A24E97897DAF313
Show »

FASTA

245

26,383

        10         20         30         40         50         60 
MAGLELLSDQ GYRVDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA VVYGPHEIRG 

        70         80         90        100        110        120 
SRARALPDRA LVNCQYSSAT FSTGERKRRP HGDRKSCEMG LQLRQTFEAA ILTQLHPRSQ 

       130        140        150        160        170        180 
IDIYVQVLQA DGGTYAACVN AATLAVLDAG IPMRDFVCAC SAGFVDGTAL ADLSHVEEAA 

       190        200        210        220        230        240 
GGPQLALALL PASGQIALLE MDARLHEDHL ERVLEAAAQA ARDVHTLLDR VVRQHVREAS 


ILLGD

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Three novel components of the human exosome." Brouwer R., Allmang C., Raijmakers R., van Aarssen Y., Egberts W.V., Petfalski E., van Venrooij W.J., Tollervey D., Pruijn G.J.M. J. Biol. Chem. 276:6177-6184(2001) [PubMed: 11110791] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], CHARACTERIZATION.
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Skin.
[4]	Bienvenut W.V. Submitted (OCT-2004) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-13, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[5]	"The yeast exosome and human PM-Scl are related complexes of 3'-->5' exonucleases." Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., Mitchell P. Genes Dev. 13:2148-2158(1999) [PubMed: 10465791] [Abstract] Cited for: CHARACTERIZATION.
[6]	"AU binding proteins recruit the exosome to degrade ARE-containing mRNAs." Chen C.-Y., Gherzi R., Ong S.-E., Chan E.L., Raijmakers R., Pruijn G.J.M., Stoecklin G., Moroni C., Mann M., Karin M. Cell 107:451-464(2001) [PubMed: 11719186] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE EXOSOME MULTIENZYME RIBONUCLEASE COMPLEX.
[7]	"Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities." Lejeune F., Li X., Maquat L.E. Mol. Cell 12:675-687(2003) [PubMed: 14527413] [Abstract] Cited for: IDENTIFICATION IN A MRNA DECAY COMPLEX WITH RENT1; RENT2 AND RENT3B.
[8]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

AF281133 mRNA. Translation: AAF82134.1.
AK000598 mRNA. Translation: BAA91279.1.
BC002777 mRNA. Translation: AAH02777.1.

IPI

IPI00745613.

RefSeq

NP_061910.1.

UniGene

Hs.632041

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2NN6	X-ray	3.35	B	2-244	[»]

SMR

Q9NPD3. Positions 7-241.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9NPD3. 20 interactions.

2-D gel databases

SWISS-2DPAGE

Q9NPD3.

Proteomic databases

PRIDE

Q9NPD3.

Genome annotation databases

Ensembl

ENSG00000178896. Homo sapiens. [Contig view]

GeneID

54512.

KEGG

hsa:54512.

NMPDR

fig|9606.3.peg.30882.

Organism-specific databases

GeneCards

GC08P145205.

H-InvDB

HIX0020970.

HGNC

HGNC:18189. EXOSC4.

MIM

606491. gene.

PharmGKB

PA134867931.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

Q9NPD3.

OMA

Q9NPD3. GDRKSTE.

Gene expression databases

ArrayExpress

Q9NPD3.

Bgee

Q9NPD3.

CleanEx

HS_EXOSC4.

GermOnline

ENSG00000178896. Homo sapiens.

Family and domain databases

InterPro

IPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
[Graphical view]

Pfam

PF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

56896.

SOURCE

Search...

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Entry information

Entry name

EXOS4_HUMAN

Accession

Primary (citable) accession number: Q9NPD3

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 2001
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 81 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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Relevant documents

Human chromosome 8

Human chromosome 8: entries, gene names and cross-references to MIM

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2-D gel databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents