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Protein

U6 snRNA-associated Sm-like protein LSm6

Gene

LSM6

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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 involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. In association with PAT1, LSM1-LSM7 binds directly to RNAs near the 3'-end and prefers oligoadenylated RNAs over polyadenylated RNAs. 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. Component of a nucleolar LSM2-LSM7 complex, which associates with the precursor of the RNA component of RNase P (pre-P RNA) and with the small nucleolar RNA (snoRNA) snR5. It may play a role in the maturation of a subset of nucleolus-associated small RNAs.6 Publications

GO - Molecular functioni

GO - Biological processi

  • maturation of SSU-rRNA Source: SGD
  • mRNA splicing, via spliceosome Source: SGD
  • tRNA processing Source: UniProtKB-KW

Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processmRNA processing, mRNA splicing, rRNA processing, tRNA processing

Enzyme and pathway databases

BioCyciYEAST:G3O-29927-MONOMER

Protein family/group databases

MoonDBiQ06406 Predicted

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm6
Gene namesi
Name:LSM6
Ordered Locus Names:YDR378C
ORF Names:D9481.18
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

SGDiS000002786 LSM6

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi74R → A: Reduces affinity for poly-U RNA ends. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001255781 – 86U6 snRNA-associated Sm-like protein LSm6Add BLAST86

Proteomic databases

MaxQBiQ06406
PaxDbiQ06406
PRIDEiQ06406

Interactioni

Subunit structurei

Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a doughnut shape. The LSm subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Except for LSM1, where a C-terminal helix crosses the ring structure to form additional interactions with LSM3 and LSM6, each subunit interacts only with its two neighboring subunits. The LSM1-LSM7 complex interacts with PAT1; within the complex PAT1 has direct interactions with LSM2 and LSM3. LSM1-LSM7 associates also with PAT1 and XRN1. Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. Component of a LSM2-LSM7 complex, which consists of at least LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. It is not known whether another protein replaces the missing LSm to form a novel heptameric complex. Component of the spliceosome U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.7 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi32437, 865 interactors
ComplexPortaliCPX-112 Lsm1-7-Pat1 complex
CPX-24 U6 snRNP complex
CPX-25 U4/U6.U5 tri-snRNP complex
CPX-32 U4/U6 snRNP
CPX-44 LSM2-8 complex
CPX-45 LSM1-7 complex
CPX-46 LSM2-7 complex
DIPiDIP-1418N
IntActiQ06406, 35 interactors
MINTiQ06406
STRINGi4932.YDR378C

Structurei

Secondary structure

186
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ06406
SMRiQ06406
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000223542
InParanoidiQ06406
KOiK12625
OMAiTQVMYIS
OrthoDBiEOG092C5VL3

Family and domain databases

InterProiView protein in InterPro
IPR016487 Lsm6/sSmF
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
PANTHERiPTHR11021 PTHR11021, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit

Sequencei

Sequence statusi: Complete.

Q06406-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSGKASTEGS VTTEFLSDII GKTVNVKLAS GLLYSGRLES IDGFMNVALS
60 70 80
SATEHYESNN NKLLNKFNSD VFLRGTQVMY ISEQKI
Length:86
Mass (Da):9,398
Last modified:May 20, 2008 - v2
Checksum:i74FE40A4509CEF33
GO

Sequence cautioni

The sequence AAB64814 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28373 Genomic DNA Translation: AAB64814.1 Different initiation.
BK006938 Genomic DNA Translation: DAA12220.1
PIRiS61173
RefSeqiNP_010666.2, NM_001180686.1

Genome annotation databases

EnsemblFungiiYDR378C; YDR378C; YDR378C
GeneIDi851984
KEGGisce:YDR378C

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U28373 Genomic DNA Translation: AAB64814.1 Different initiation.
BK006938 Genomic DNA Translation: DAA12220.1
PIRiS61173
RefSeqiNP_010666.2, NM_001180686.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80e1-86[»]
4C8QX-ray3.70F1-86[»]
4C92X-ray2.30F1-86[»]
4M75X-ray2.95D/K1-86[»]
4M77X-ray3.11D/K1-86[»]
4M78X-ray2.79D/K1-86[»]
4M7AX-ray2.78D/K1-86[»]
4M7DX-ray2.60D/K1-86[»]
5GANelectron microscopy3.6061-86[»]
5NRLelectron microscopy7.20z1-86[»]
5VSUX-ray3.10F1-86[»]
5ZWMelectron microscopy3.40x1-86[»]
5ZWOelectron microscopy3.90x1-86[»]
6ASOX-ray2.71F1-86[»]
ProteinModelPortaliQ06406
SMRiQ06406
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32437, 865 interactors
ComplexPortaliCPX-112 Lsm1-7-Pat1 complex
CPX-24 U6 snRNP complex
CPX-25 U4/U6.U5 tri-snRNP complex
CPX-32 U4/U6 snRNP
CPX-44 LSM2-8 complex
CPX-45 LSM1-7 complex
CPX-46 LSM2-7 complex
DIPiDIP-1418N
IntActiQ06406, 35 interactors
MINTiQ06406
STRINGi4932.YDR378C

Protein family/group databases

MoonDBiQ06406 Predicted

Proteomic databases

MaxQBiQ06406
PaxDbiQ06406
PRIDEiQ06406

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR378C; YDR378C; YDR378C
GeneIDi851984
KEGGisce:YDR378C

Organism-specific databases

SGDiS000002786 LSM6

Phylogenomic databases

HOGENOMiHOG000223542
InParanoidiQ06406
KOiK12625
OMAiTQVMYIS
OrthoDBiEOG092C5VL3

Enzyme and pathway databases

BioCyciYEAST:G3O-29927-MONOMER

Miscellaneous databases

PROiPR:Q06406

Family and domain databases

InterProiView protein in InterPro
IPR016487 Lsm6/sSmF
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
PANTHERiPTHR11021 PTHR11021, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLSM6_YEAST
AccessioniPrimary (citable) accession number: Q06406
Secondary accession number(s): D6VT10
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: May 20, 2008
Last modified: November 7, 2018
This is version 161 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names
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Main funding by: National Institutes of Health

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