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Protein

U6 snRNA-associated Sm-like protein LSm5

Gene

LSM5

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. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. 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 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved in degradation of nuclear pre-mRNA by targeting them for decapping. LSM5 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM5, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.7 Publications

GO - Molecular functioni

GO - Biological processi

  • mRNA splicing, via spliceosome Source: SGD
  • nuclear-transcribed mRNA catabolic process Source: SGD
  • rRNA processing Source: UniProtKB-KW
  • 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-30307-MONOMER
ReactomeiR-SCE-430039 mRNA decay by 5' to 3' exoribonuclease

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm5
Gene namesi
Name:LSM5
Ordered Locus Names:YER146W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER146W
SGDiS000000948 LSM5

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

Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi74S → A: Slightly increases affinity for poly-U RNA ends. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001255741 – 93U6 snRNA-associated Sm-like protein LSm5Add BLAST93

Proteomic databases

MaxQBiP40089
PaxDbiP40089
PRIDEiP40089
TopDownProteomicsiP40089

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. 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. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. 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. Interacts with PAT1.7 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi36895, 67 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-1417N
IntActiP40089, 34 interactors
MINTiP40089
STRINGi4932.YER146W

Structurei

Secondary structure

193
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 13Combined sources6
Turni15 – 17Combined sources3
Beta strandi18 – 37Combined sources20
Beta strandi43 – 52Combined sources10
Beta strandi62 – 66Combined sources5
Beta strandi69 – 73Combined sources5
Beta strandi77 – 83Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80f1-93[»]
4C8QX-ray3.70E1-93[»]
4C92X-ray2.30E1-93[»]
4M75X-ray2.95E/L1-93[»]
4M77X-ray3.11E/L1-93[»]
4M78X-ray2.79E/L1-93[»]
4M7AX-ray2.78E/L1-93[»]
4M7DX-ray2.60E/L1-93[»]
5GANelectron microscopy3.6051-93[»]
5NRLelectron microscopy7.20o1-93[»]
5VSUX-ray3.10E1-93[»]
6ASOX-ray2.71E1-93[»]
ProteinModelPortaliP40089
SMRiP40089
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

GeneTreeiENSGT00390000001455
HOGENOMiHOG000223547
InParanoidiP40089
KOiK12624
OMAiCMLIPGS
OrthoDBiEOG092C5VL3

Family and domain databases

CDDicd01732 LSm5, 1 hit
InterProiView protein in InterPro
IPR033871 LSm5
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
PANTHERiPTHR20971 PTHR20971, 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.

P40089-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLPEILPLE VIDKTINQKV LIVLQSNREF EGTLVGFDDF VNVILEDAVE
60 70 80 90
WLIDPEDESR NEKVMQHHGR MLLSGNNIAI LVPGGKKTPT EAL
Length:93
Mass (Da):10,423
Last modified:February 1, 1995 - v1
Checksum:i84E8A1E8E2F078FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18917 Genomic DNA Translation: AAB64673.1
AY557783 Genomic DNA Translation: AAS56109.1
BK006939 Genomic DNA Translation: DAA07807.1
PIRiS50649
RefSeqiNP_011073.1, NM_001179036.1

Genome annotation databases

EnsemblFungiiYER146W; YER146W; YER146W
GeneIDi856889
KEGGisce:YER146W

Similar proteinsi

Entry informationi

Entry nameiLSM5_YEAST
AccessioniPrimary (citable) accession number: P40089
Secondary accession number(s): D3DM53
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: June 20, 2018
This is version 155 of the entry and version 1 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

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