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P62312 (LSM6_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 96. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
U6 snRNA-associated Sm-like protein LSm6
Gene names
Name:LSM6
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length80 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA By similarity.

Subunit structure

Component of the heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. Component of the heptameric LSM2-LSM8 complex, which consists of LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. The LSm subunits form a seven-membered ring structure with a doughnut shape. Ref.2 Ref.7

Subcellular location

Cytoplasm. Nucleus By similarity Ref.7.

Sequence similarities

Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
rRNA processing
tRNA processing
   Cellular componentCytoplasm
Nucleus
Spliceosome
   LigandRNA-binding
   Molecular functionRibonucleoprotein
   PTMAcetylation
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processRNA metabolic process

Traceable author statement. Source: Reactome

RNA splicing

Traceable author statement Ref.2. Source: UniProtKB

exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Traceable author statement. Source: Reactome

gene expression

Traceable author statement. Source: Reactome

mRNA metabolic process

Traceable author statement. Source: Reactome

mRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

Traceable author statement. Source: Reactome

rRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

tRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytosol

Traceable author statement. Source: Reactome

small nuclear ribonucleoprotein complex

Traceable author statement Ref.2. Source: UniProtKB

spliceosomal complex

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionpoly(A) RNA binding

Inferred from direct assay PubMed 22681889. Source: UniProtKB

protein binding

Inferred from physical interaction PubMed 15231747PubMed 22365833. Source: IntAct

Complete GO annotation...

Binary interactions

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 8080U6 snRNA-associated Sm-like protein LSm6
PRO_0000125575

Amino acid modifications

Modified residue591N6-acetyllysine Ref.8

Sequences

Sequence LengthMass (Da)Tools
P62312 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 21167891FDE804F1

FASTA809,128
        10         20         30         40         50         60 
MSLRKQTPSD FLKQIIGRPV VVKLNSGVDY RGVLACLDGY MNIALEQTEE YVNGQLKNKY 

        70         80 
GDAFIRGNNV LYISTQKRRM 

« Hide

References

« Hide 'large scale' references
[1]"Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro."
Achsel T., Brahms H., Kastner B., Bachi A., Wilm M., Luehrmann R.
EMBO J. 18:5789-5802(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE LSM2-LSM8 COMPLEX.
[3]"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. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]"Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. expand/collapse author list , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Uterus.
[7]"The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci."
Ingelfinger D., Arndt-Jovin D.J., Luehrmann R., Achsel T.
RNA 8:1489-1501(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, IDENTIFICATION IN THE LSM1-LSM7 COMPLEX.
[8]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ238098 mRNA. Translation: CAB45869.1.
AF182292 mRNA. Translation: AAD56230.1.
AK312126 mRNA. Translation: BAG35062.1.
AC097372 Genomic DNA. Translation: AAY41032.1.
CH471056 Genomic DNA. Translation: EAX05029.1.
CH471056 Genomic DNA. Translation: EAX05030.1.
CH471056 Genomic DNA. Translation: EAX05031.1.
BC016026 mRNA. Translation: AAH16026.1.
CCDSCCDS3767.1.
RefSeqNP_009011.1. NM_007080.2.
UniGeneHs.190520.

3D structure databases

ProteinModelPortalP62312.
SMRP62312. Positions 7-74.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116328. 22 interactions.
DIPDIP-31128N.
IntActP62312. 15 interactions.
MINTMINT-4100591.
STRING9606.ENSP00000296581.

PTM databases

PhosphoSiteP62312.

Polymorphism databases

DMDM61227727.

Proteomic databases

MaxQBP62312.
PaxDbP62312.
PeptideAtlasP62312.
PRIDEP62312.

Protocols and materials databases

DNASU11157.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000296581; ENSP00000296581; ENSG00000164167.
ENST00000502781; ENSP00000422392; ENSG00000164167.
ENST00000504181; ENSP00000420929; ENSG00000164167.
ENST00000515311; ENSP00000427036; ENSG00000164167.
GeneID11157.
KEGGhsa:11157.
UCSCuc003ikq.4. human.

Organism-specific databases

CTD11157.
GeneCardsGC04P147097.
HGNCHGNC:17017. LSM6.
HPAHPA045079.
MIM607286. gene.
neXtProtNX_P62312.
PharmGKBPA128394584.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1958.
HOVERGENHBG052369.
InParanoidP62312.
KOK12625.
OMAEMETENM.
OrthoDBEOG7HXCTK.
PhylomeDBP62312.
TreeFamTF313751.

Enzyme and pathway databases

ReactomeREACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

BgeeP62312.
CleanExHS_LSM6.
GenevestigatorP62312.

Family and domain databases

InterProIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamPF01423. LSM. 1 hit.
[Graphical view]
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

GeneWikiLSM6.
GenomeRNAi11157.
NextBio42433.
PROP62312.
SOURCESearch...

Entry information

Entry nameLSM6_HUMAN
AccessionPrimary (citable) accession number: P62312
Secondary accession number(s): Q4W5J5, Q9Y4Y8
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: July 9, 2014
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

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

Human chromosome 4

Human chromosome 4: entries, gene names and cross-references to MIM