View source for Lsm

<StructureSection load='3pgw' size='400' side='right' scene='Sandbox_502/U1_sm_ring/2' caption='Human U1 snRNP [[3pgw]]'>
='''Lsm Protein Structure'''=

by Kelly Hrywkiw
__TOC__

=Introduction=

Sm-like ([http://en.wikipedia.org/wiki/LSm Lsm]) proteins most closely resemble Sm proteins, both of which are found in the three domains of life <ref name ="wu">PMID:22615807</ref>.  Sm proteins play a large role in [http://en.wikipedia.org/wiki/Spliceosome spliceosome] biogenesis through mediating U1, U2, U4, U5, and U6 [http://en.wikipedia.org/wiki/SnRNP snRNP assembly]<ref name ="he">PMID:10801455</ref>.  The <scene name='Sandbox_502/U1_sm_ring/2'>Sm ring</scene> of proteins can be broken down into seven specific proteins (SmB, SmD1, SmD2, SmD3, SmE, SmF, and SmG in humans) all of which share a conserved Sm motif that is also found in the Lsm proteins<ref name ="he"/><ref name ="naidoo"/>. Eukaryotes have 16 or more Lsm proteins encoded in their genome, in contrast archaeal species have only one to three <ref name ="naidoo">PMID:18329667</ref>.  A total of nine specific Lsm proteins are found in yeast (Lsm1-Lsm9).  The Lsm proteins 2-7 most closely resemble Sm proteins D1-G, where Lsm 1 and 8 most closely resemble the SmB protein <ref name ="he"/>.  Lsm9 does not appear to resemble any of the Sm proteins, although there have been some related structures found in the archaeal genome <ref name ="he"/>.  Several studies have shown that the Sm proteins form into seven membered rings which bind to the Sm binding site, a U rich sequence found in all but U6 snRNA<ref name ="he"/>.  Lsm proteins can form homomeric rings of heptamers, hexamers, or octamers<ref name ="wu"/>.  In addition they have been found to predominately associate into three complexes: Lsm2-8, Lsm1-7, and Lsm2-7 <ref name ="wu"/>.  The exact functionality of these complexes is in either [http://en.wikipedia.org/wiki/RNA_splicing pre-mRNA splicing], [http://en.wikipedia.org/wiki/Messenger_RNA#Degradation mRNA decay] or other roles, and is dictated by their composition, structure, and cellular location <ref name ="wu"/><ref name ="he"/>. 


==The Different Lsm Complexes==

Evidence suggests that there are two main Lsm complexes, Lsm1-7 which is associated with mRNA decay, and Lsm 2-8 which is associated with pre-mRNA splicing<ref name ="wu"/><ref name ="he"/>.  The first piece of evidence to suggest different roles is the cellular localization of the different Lsm complexes<ref name ="wu"/>.  For example, Lsm1 is predominantly cytoplasmic (where mRNA degradation takes place), as is the Lsm1-7 complex<ref name ="wu"/>.  The Lsm complex 2-8 is most likely nuclear because that is the location of U6 snRNP assembly <ref name ="pannone">PMID:10898971</ref>.  In addition, mutation experiments have shown that while Lsm2 to Lsm7 mutants have altered mRNA decay and splicing function, Lsm1 and Lsm8 mutants only have altered mRNA decay and pre-mRNA splicing function respectively <ref name ="he"/>.  Further evidence is found in [http://en.wikipedia.org/wiki/Immunoprecipitation immunopercipitation] experiments.  For example, while Lsm2 to Lsm7 co-immunopercipitate with both U6 snRNA and with mRNA decay factors, Lsm1 and Lsm8 only co-immunopercipitate mRNA degradation factors and U6 snRNA respectively <ref name ="he"/>.   Due to the difference in functionality of either Lsm1 or Lsm8 it is interesting to note that Lsm1 and Lsm8 are both closely related structurally to the SmB protein<ref name ="he"/>.  

==Role in Pre-mRNA splicing==

The processing of [http://en.wikipedia.org/wiki/Pre-mRNA pre-mRNA] takes place through the use of a large dynamic machine known as the spliceosome, through which [http://en.wikipedia.org/wiki/Intron introns] are removed and [http://en.wikipedia.org/wiki/Exon exons] are spliced together to create a mature [http://en.wikipedia.org/wiki/MRNA mRNA]<ref name ="architecture of"/><ref name ="structure and function">PMID:19000813</ref>.  The spliceosome is comprised of five [http://en.wikipedia.org/wiki/SnRNA snRNA] molecules (snRNAs U1, U2, U4, U5, and U6) and over one hundred associated proteins<ref name ="architecture of"/><ref name ="structure and function"/>.  Assembly of the spliceosome is thought to take place in a stepwise manner around the pre-mRNA transcript<ref name ="architecture of"/><ref name ="structure and function"/>.  The first step involves recognition of the 5’ splice site by U1 snRNP, followed by recognition of the branch point sequence by U2 snRNP<ref name ="architecture of"/><ref name ="structure and function"/>.  From this point the remaining snRNPs U4, U5, and U6 join as a preformed tri-snNRP<ref name ="architecture of"/><ref name ="structure and function"/>.  Together the five snRNPs form the precatalytic spliceosome which must undergo a series of changes before it can actively splice<ref name ="structural evidence">PMID:19525970</ref><ref name ="structure and function"/><ref name ="common design">PMID:19525970</ref><ref name ="architecture of">PMID:22471593</ref>.

The Lsm complex 2-8 is involved in pre-mRNA splicing through association with the 3’terminal poly(U) tract of U6 snRNA <ref name="pannone"/>.  U6 snRNP is different from the other snRNPs because it is completely assembled in the [http://en.wikipedia.org/wiki/Cell_nucleus nucleus], whereas the other snRNAs first travel to the [http://en.wikipedia.org/wiki/Cytoplasm cytoplasm] <ref name ="pannone"/><ref name ="architecture of"/>.  While the exact mechanism by which the Lsm2-8 complex acts is unclear, it is thought that it provides stability and function to the U6 snRNP<ref name ="he"/>.  For example, several experiments using mutants with point mutations in the Lsm proteins 2-8 have shown defects in splicing that correlate with low levels of U6 snRNA <ref name ="he"/>.  It may also play a role in the various rearrangements that are necessary throughout the splicing cycle, and has been shown to be important in the assembly of U4-U6 di snRNP and U4-U5/U6 tri snRNP <ref name ="he"/>.   An interesting difference between the Sm and Lsm proteins is that in order to assemble the Sm ring RNA must be present, yet this is not a requirement in Lsm ring assembly <ref name ="pannone"/>.  Overall, there is significant evidence to suggest that the Lsm proteins 2-8 play a key role in spliceosome biogenesis and architecture.    

==Role in mRNA decay==

In yeast degradation of mRNA takes place by first shortening the poly(A) tail then the removing the 5’cap by [[4a53|Dcp1]], a decapping protein <ref name ="pannone"/>.  The major exoribonuclease in mRNA decay ([[2y35|Xrn1]]) then quickly degrades the decapped mRNA <ref name ="pannone"/>.  Interestingly, when the Lsm 1-7 complex is purified Xrn1, Dcp1, Mrt1 (an additional protein associated with mRNA decapping), and mRNA co-immunopercipitate <ref name ="pannone"/>.  However, it is not only Lsm 1 that plays a role in mRNA decay.  Lsm mutants of the 2-7 proteins have increased amounts of capped, deadenylated mRNAs <ref name ="pannone"/>.  There are two postulated functions of the Lsm1-7 complex in mRNA decay.  The first suggests that the Lsm ring binds to the mRNA first then recruits the Dcp1, the second function may be to facilitate rearrangements of the mRNP complex to allow decapping enzymes access to the 5’cap <ref name ="he"/>.  Lsm proteins therefore do not only appear to play a role in creating functional mRNA, but also in degradation of mature mRNA.  

==Other roles of Lsm proteins==

A third complex of Lsm proteins (Lsm2-7) is found in the nucleoli of Saccharomyces cerecisiae <ref name ="wu"/>.  It is believed to play a role in the function or biogenesis of snoRNAs.  Other potential roles of the Lsm proteins include processing of tRNAs, snoRNAs, and rRNAs, histone mRNA decapping, miRNA biogenesis, and maturation and/or stabilization of nascent RNA polymerase III transcripts <ref name ="wu"/><ref name ="he"/>.  

=Structure of Lsm proteins=

<scene name='Sandbox_502/Splsm3start/1'>Sm and Lsm proteins both exhibit the Sm motif</scene>, which consist of an <scene name='Sandbox_502/Splsm3_alpha/2'>N-terminal</scene> [http://en.wikipedia.org/wiki/Alpha_helix α-helix] proceeded by a twisted <scene name='Sandbox_502/Splsm3_beta/2'>five stranded </scene>[http://en.wikipedia.org/wiki/Beta_sheet β-sheet] <ref name ="wu"/><ref name ="naidoo"/>.  <scene name='Sandbox_502/Sclsm3/3'>Loop L4</scene>, located between stands <scene name='Sandbox_502/Sclsm3b3/2'>β3</scene> and <scene name='Sandbox_502/Sclsm3b4/1'>β4</scene> of the β sheet, varies between 3 to 30 residues in length across the different Lsm proteins <ref name ="naidoo"/>.  The β-sheet encloses a set of hydrophobic residues <ref name ="naidoo"/>.  When the Lsm ring is assembled the hydrophobic region spreads into the now adjacent Lsm protein monomers <ref name ="naidoo"/>.  When assembled into the ring between each subunit there are hydrogen bonds formed between <scene name='Sandbox_502/Sclsm3b4ofa/2'>β4 of one subunit</scene> and <scene name='Sandbox_502/Sclsm3b4ofb/2'>β5 of the neighboring subunit</scene> <ref name ="naidoo"/>.  These interactions provided the Lsm ring with enough contacts to make a very stable structure <ref name ="naidoo"/>.  There are two sides to the ring, the helix face and the loop face, found on <scene name='Sandbox_502/Splsm3helixface/4'>opposite sides</scene>  of the ring <ref name ="wu"/>.  It has been postulated that a U-rich RNA may bind to the inner portion of the helix face, and take part in hydrogen bonding interactions with residues located on loops 3 and 5, as well as potentially pass through the <scene name='Sandbox_502/Splsm3pore/2'>pore</scene> itself <ref name ="naidoo"/>.  

It is possible for single Lsm proteins to form homomeric heptamers, hexamers, or octamers, as well as the Lsm1-7 or 2-8 hexamers.  In addition, Lsm proteins have been found to form higher order quaternary structures during the crystallization process <ref name ="naidoo"/><ref name ="wu"/>.  These interactions are formed between helix-helix faces, loop-loop faces, and helix-loop faces <ref name ="naidoo"/>.  The crystal structures available for analysis do not consist of full Lsm1-7 or Lsm2-8 complexes.  However, the Lsm3 monomer, the N-terminal region of Lsm4, and an Lsm complex Lsm5-7 have been crystallized. 



==Lsm 3==

The Lsm3 protein had been crystalized from Schizosaccharomyces pombe and from Saccharomyces cerevisiae, hereby referred to as SpLsm3 and ScLsm3 at 2.7Å and 2.5Å respectively. 

===ScLsm3===

The ScLsm3 crystal structure takes the form of a ring composed of eight monomeric subunits.  Each monomer contains the Sm motif containing the N-terminal α-helix (pro4-leu10) and the curved β-sheet (Glu14-Ser77).  The stands β3 and β4 are long, which causes loop L4 residues to stick out and twist away from the main body of the ring.  The only other Sm/Lsm protein to exhibit this is the human Sm protein SmB.  Between each of the subunits there are hydrogen interactions between the C-terminal region of β4 and the neighboring β5.  In addition, there are <scene name='Sandbox_502/Sclsm3residues/1'>hydrophobic residues</scene> buried at this interface, which include Phe67, Ile68, Thr74, and Ile76.  The overall ring structure is approximately 75Å wide, 50Å thick.  The pore is approximately 20Å at the helix face and 25Å at the loop face.  These measurements are greater than those of six or seven membered Lsm rings <ref name ="naidoo"/>.



===SpLsm3===

As in ScLsm3, <scene name='Sandbox_502/Splsm3/4'>SpLsm3</scene> exhibits the sm motif containing an N-terminal α-helix (residues 10-17) and a curved β-sheet (residues 19-89).  However, rather than forming an octomeric ring structure it formed a heptameric ring structure in crystallization experiments.  SpLsm3 monomers interact through the same β4-β5 pairing as in ScLsm3.  The overall ring is 61.5Å wide, 31Å thick, where the pore is approximately 20.7Å wide.  In this crystal structure loop four is distorted<ref name ="wu"/>. 







==Lsm 4==

The <scene name='Sandbox_502/Splsm4/2'>Lsm4 crystal structure</scene> contains a trimer of the Lsm4 monomers.  It contains the Sm motif consisting of an α-helix (distorted) and a β-sheet formed by five antiparallel stands (residues 14-70)<ref name ="wu"/>.





==Lsm 5/6/7==
<scene name='Sandbox_502/Splsm657m/1'>Lsm 5/6/7</scene> 

A 2.5Å resolution structure of Lsm5, Lsm6 and Lsm7 has been determined where the crystal contains two hexameric Lsm657-657 rings.  <scene name='Sandbox_502/Splsm657m5/1'>Lsm5</scene> is located between <scene name='Sandbox_502/Splsm657m6/2'>Lsm6</scene> and <scene name='Sandbox_502/Splsm657m7/1'>Lsm7</scene> which analogous to their Sm counters parts.  In the hexameric ring each subunit interacts in the same manner as the other Lsm proteins (ie through the β4 stand of one subunit to the β5 strand of the other) to form a continuous β-sheet through the whole ring.  Each of the Lsm proteins exhibits the Sm motif with very small differences seen between them <ref name ="mund">PMID:22001694</ref>. 

===Role in RNA binding===

With respect to the role of Lsm proteins binding to RNA substrates, the pore of the Lsm657-657 ring is positively charged, which would confer to interactions with negatively charged RNA.  The Sm ring of Archaeoglobus fulgidus in complex with polyU RNA shows that each of the Sm proteins interacts with one base of RNA through residues in loops 3 and 5, and that the RNA is passed through the pore.  Due to the fact that the residues between the Sm and Lsm proteins are fairly conserved it is possible that the Lsm proteins act through a similar mechanism.  Two main differences can be seen however. There should be a canonical arginine or lysine in loop five of Lsm5 that forms a hydrogen bond to a base in the RNA, yet there is an asparagine present.  In addition, a canonical aromatic residue that provides stacking interactions with an RNA base should be found in loop three of Lsm7, however there is a leucine present instead.  While these differences prevent one from applying the RNA-protein interactions of Sm proteins to Lsm proteins, future studies may elucidate the exact mechanism <ref name ="mund">PMID:22001694</ref>.  

</StructureSection>
=Additional Resources=

*[http://www.rcsb.org/pdb/explore/explore.do?structureId=3BW1 Crystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=4EMK Crystal structure of SpLsm5/6/7, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=4EMG Crystal structure of SpLsm3, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=4EMH Crystal structure of SpLsm4, in the RCSB Protein Data Bank]
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=3SWN Structure of the LSm657 Complex: An Assembly Intermediate of the LSm1 7 and LSm2 8 Rings, in the RCSB Protein Data Bank]

=References=
<References/>