SMD3/YLR147C Summary Help

Standard Name SMD3
Systematic Name YLR147C
Alias SLT16 1
Feature Type ORF, Verified
Description Core Sm protein Sm D3; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm D3 (2, 3 and see Summary Paragraph)
Gene Product Alias Sm D3 2
Chromosomal Location
ChrXII:434463 to 434158 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gene Ontology Annotations All SMD3 GO evidence and references
  View Computational GO annotations for SMD3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Large-scale survey
141 total interaction(s) for 72 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 120
  • Affinity Capture-RNA: 3
  • Co-purification: 3
  • Two-hybrid: 11

Genetic Interactions
  • Synthetic Growth Defect: 1
  • Synthetic Lethality: 3

Expression Summary
Length (a.a.) 101
Molecular Weight (Da) 11,224
Isoelectric Point (pI) 10.78
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXII:434463 to 434158 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..306 434463..434158 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000004137

The Sm and Sm-like (Lsm) proteins are a highly conserved family of ancient origin, found in bacteria, archaea, and eukaryotes. These proteins were first characterized in humans with systemic lupus erythemathosus, where autoantibodies were found that recognize an antigen called Sm. The Sm antigen was characterized as a domain present in a group of eight small proteins (alternatively spliced products B and B', as well as D1, D2, D3, E, F, and G) that associated with four of the five snRNAs (U1, U2, U4, and U5, but not U6) involved in splicing of nuclear pre-mRNAs (4). The S. cerevisiae genome contains 16 proteins containing an Sm, or Sm-like, domain. Seven genes encode proteins corresponding to the human Sm antigen proteins: SMB1 (Sm B), SMD1 (Sm D1), SMD2 (Sm D2), SMD3 (Sm D3), SME1 (Sm E), SMX3 (Sm F), and SMX2 (Sm G). An additional eight genes, LSM1, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, and LSM8 also encode proteins containing Sm domains and are thus named LSM (Like SM) proteins. These proteins are more closely related to individual Sm proteins than to each other. MAK31 has also been reported to contain an Sm domain (4).

Crystal structures of human Sm proteins, in pairs or with U1 snRNA, indicate that the seven core Sm proteins form a heteroheptameric ring with a small central hole (5, 6, 7). The Sm site, the conserved uridine rich sequence found near the 3-prime ends of the U1, U2, U4, and U5 snRNAs, appears to form contacts along the inner surface of the ring complex and it is suggested that the RNA may pass through the hole (5, 6, 7). Experiments in S. cerevisiae indicate that a similar seven-membered ring containing one copy of each of the seven Sm proteins exists in yeast (8). Similarly to the Sm proteins, the Lsm proteins also form heteroheptameric rings. In S. cerevisiae, as well as in other eukaryotes, two different Lsm ring complexes exist, containing Lsm2p-7p and either Lsm1p or Lsm8p (3).

The Sm ring complex is required for the biogenesis of the U1, U2, U4, and U5 snRNPs and also has additional functions during splicing of nuclear mRNAs. Depletion of a single Sm protein, e.g. Smd3p, decreases total levels of U1, U2, U4, and U5 as well as the amount of these snRNAs which have been processed to contain the normal trimethyl cap structure (9). Similarly, destroying the Sm binding site in an snRNA also prevents proper processing and capping of the snRNA (10). It is not yet clear whether the snRNAs are exported to the cytoplasm for assembly into snRNP complexes, as occurs in mammalian cells, or whether the snRNA remains in the nucleus and the Sm ring complex is imported into the nucleus to bind with the snRNA (11, 12). Tgs1p associates with the SmB protein of the Sm ring to hypermethylate the snRNA cap structure, a process which occurs in the nuceolus (12). The Sm ring complex remains associated with the snRNA as part of the core of each snRNP, each of which contains additional specific proteins.

The Sm ring complex is also associated with the telomerase template RNA (the product of the TLC1 gene) and appears to be involved in biogenesis of the telomerase enzyme in yeast. After the RNA subunit is transcribed, capped, and polyadenylated, binding by the Sm ring complex to an Sm site in the 3' region of the TLC1 RNA appears to be required for further processing, including removal of the polyA tail and hypermethylation of the cap. As in the case of the spliceosomal snRNPs, it appears that the Sm complex remains associated with the telomerase RNA in the active holo-telomerase enzyme (13).

Last updated: 2006-01-26 Contact SGD

References cited on this page View Complete Literature Guide for SMD3
1) Xu D, et al.  (1998) Synthetic lethality of yeast slt mutations with U2 small nuclear RNA mutations suggests functional interactions between U2 and U5 snRNPs that are important for both steps of pre-mRNA splicing. Mol Cell Biol 18(4):2055-66
2) Burge CB et al.  (1999) "Splicing of precursors to mRNAs by the spliceosomes." Pp. 525-560 in The RNA World, Second Edition, edited by Gesteland RF, Cech TR, Atkins JF. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
3) Beggs JD  (2005) Lsm proteins and RNA processing. Biochem Soc Trans 33(Pt 3):433-8
4) Salgado-Garrido J, et al.  (1999) Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J 18(12):3451-62
5) Kambach C, et al.  (1999) Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 96(3):375-87
6) Stark H, et al.  (2001) Arrangement of RNA and proteins in the spliceosomal U1 small nuclear ribonucleoprotein particle. Nature 409(6819):539-42
7) Pomeranz Krummel DA, et al.  (2009) Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution. Nature 458(7237):475-80
8) Walke S, et al.  (2001) Stoichiometry of the Sm proteins in yeast spliceosomal snRNPs supports the heptamer ring model of the core domain. J Mol Biol 308(1):49-58
9) Roy J, et al.  (1995) Structurally related but functionally distinct yeast Sm D core small nuclear ribonucleoprotein particle proteins. Mol Cell Biol 15(1):445-55
10) Seipelt RL, et al.  (1999) U1 snRNA is cleaved by RNase III and processed through an Sm site-dependent pathway. Nucleic Acids Res 27(2):587-95
11) Bordonne R  (2000) Functional characterization of nuclear localization signals in yeast Sm proteins. Mol Cell Biol 20(21):7943-54
12) Mouaikel J, et al.  (2002) Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus. Mol Cell 9(4):891-901
13) Seto AG, et al.  (1999) Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle. Nature 401(6749):177-80