P62312 (LSM6_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
U6 snRNA-associated Sm-like protein LSm6

Gene names

Name:

LSM6

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	80 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	mRNA processing mRNA splicing rRNA processing tRNA processing
Cellular component	Cytoplasm Nucleus Spliceosome
Ligand	RNA-binding
Molecular function	Ribonucleoprotein
PTM	Acetylation
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	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 mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW rRNA processing Inferred from electronic annotation. Source: UniProtKB-KW tRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytosol 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_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
LSM3	P62310	3	EBI-373310,EBI-348239
LSM5	Q9Y4Y9	3	EBI-373310,EBI-373007
LSM7	Q9UK45	3	EBI-373310,EBI-348372

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 80	80	U6 snRNA-associated Sm-like protein LSm6		PRO_0000125575
Amino acid modifications
	Modified residue	59	1	N6-acetyllysine Ref.8

Sequences

	Sequence		Length	Mass (Da)
	P62312 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 21167891FDE804F1	FASTA	80	9,128
	10 20 30 40 50 60 MSLRKQTPSD FLKQIIGRPV VVKLNSGVDY RGVLACLDGY MNIALEQTEE YVNGQLKNKY 70 80 GDAFIRGNNV LYISTQKRRM

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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, MASS SPECTROMETRY.
[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.
IPI	IPI00001146.
RefSeq	NP_009011.1. NM_007080.2.
UniGene	Hs.190520.
3D structure databases
ProteinModelPortal	P62312.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-31128N.
IntAct	P62312. 12 interactions.
STRING	9606.ENSP00000296581.
PTM databases
PhosphoSite	P62312.
Polymorphism databases
DMDM	61227727.
Proteomic databases
PaxDb	P62312.
PeptideAtlas	P62312.
PRIDE	P62312.
Protocols and materials databases
DNASU	11157.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000296581; ENSP00000296581; ENSG00000164167. ENST00000502781; ENSP00000422392; ENSG00000164167. ENST00000504181; ENSP00000420929; ENSG00000164167. ENST00000515311; ENSP00000427036; ENSG00000164167.
GeneID	11157.
KEGG	hsa:11157.
UCSC	uc003ikq.4. human.
Organism-specific databases
CTD	11157.
GeneCards	GC04P147097.
HGNC	HGNC:17017. LSM6.
HPA	HPA045079.
MIM	607286. gene.
neXtProt	NX_P62312.
PharmGKB	PA128394584.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG1958.
HOVERGEN	HBG052369.
InParanoid	P62312.
KO	K12625.
OMA	YISTSTK.
OrthoDB	EOG4Q2DH6.
PhylomeDB	P62312.
Enzyme and pathway databases
Reactome	REACT_21257. Metabolism of RNA. REACT_71. Gene Expression.
Gene expression databases
ArrayExpress	P62312.
Bgee	P62312.
CleanEx	HS_LSM6.
Genevestigator	P62312.
GermOnline	ENSG00000164167. Homo sapiens.
Family and domain databases
InterPro	IPR010920. LSM_dom. IPR001163. Ribonucl_LSM. IPR006649. Ribonucl_LSM_euk/arc. [Graphical view]
Pfam	PF01423. LSM. 1 hit. [Graphical view]
SMART	SM00651. Sm. 1 hit. [Graphical view]
SUPFAM	SSF50182. Sm_like_riboprot. 1 hit.
ProtoNet	Search...
Other
GenomeRNAi	11157.
NextBio	42433.
SOURCE	Search...

Entry information

Entry name

LSM6_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.