Structure LSm

1 structure

1.1 secondary
1.2 tertiary
1.3 quaternary
1.4 rna oligonucleotide binding

structure

lsm secondary structure showing n-terminal alpha helix , five-strand antiparallel beta sheet.



the lsm protein human smd1 showing eight-strand beta sandwich peptide backbone description. (the beta sheet fold hinge runs along bottom of image.)

uridine phosphate binds in archaeal sm1 between β2b/β3a loop , β4b/β5 loop. uracil stacked between histidine , arginine residues, stabilized hydrogen bonding asparagine residue, , hydrogen bonding between aspartate residue , ribose. lsm proteins characterized beta sheet (the secondary structure), folded lsm fold (the tertiary structure), polymerization 6 or 7 member torus (the quaternary structure), , binding rna oligonucleotides. modern paradigm classifies proteins on basis of protein structure , active field, 3 major approaches, scop (structural classification of proteins), cath (class, architecture, topology, homologous superfamily), , fssp/dali (families of structurally similar proteins).

secondary

the secondary structure of lsm protein small five-strand anti-parallel beta sheet, strands identified n-terminal end c-terminal end β1, β2, β3, β4, β5. scop class of beta proteins , cath class of beta defined protein structures beta sheets, including lsm. sm1 sequence motif corresponds β1, β2, β3 strands, , sm2 sequence motif corresponds β4 , β5 strands. first 4 beta strands adjacent each other, β5 adjacent β1, turning overall structure short barrel. structural topology described 51234. short (two 4 turns) n-terminal alpha helix present in lsm proteins. β3 , β4 strands short in lsm proteins, , separated unstructured coil of variable length. β2, β3 , β4 strands bent 120° degrees @ midpoints bends in these strands glycine, , side chains internal beta barrel hydrophobic residues valine, leucine, isoleucine , methionine.

tertiary

scop classifies lsm structure sm-like fold, 1 of 149 different beta protein folds, without intermediate groupings. lsm beta sheet sharply bent , described roll architecture in cath (one of 20 different beta protein architectures in cath). 1 of beta strands (β5 in lsm) crosses open edge of roll form small sh3 type barrel topology (one of 33 beta roll topologies in cath). cath lists 23 homologous superfamilies sh3 type barrel topology, 1 of lsm structure (rna binding protein in cath system). scop continues structural classification after fold superfamily, family , domain, while cath continues sequence family, these divisions more appropriately described in evolution , phylogeny section.

the sh3-type barrel tertiary structure of lsm fold formed bent (about 120°) β2, β3 , β4 strands, barrel structure closed β5 strand. emphasizing tertiary structure, each bent beta strand can described 2 shorter beta strands. lsm fold can viewed eight-strand anti-parallel beta sandwich, 5 strands in 1 plane , 3 strands in parallel plane 45° pitch angle between 2 halves of beta sandwich. short (two 4 turns) n-terminal alpha helix occurs @ 1 edge of beta sandwich. alpha helix , beta strands can labeled (from n-terminus c-terminus) α, β1, β2a, β2b, β3a, β3b, β4a, β4b, β5 , b refer either 2 halves of bent strand in five-strand description, or individual strands in eight-strand description. each strand (in eight-strand description) formed 5 amino acid residues. including bends , loops between strands, , alpha helix, 60 amino acid residues contribute lsm fold, varies between homologs due variation in inter-strand loops, alpha helix, , lengths of β3b , β4a strands.

quaternary

lsm proteins typically assemble lsm ring, 6 or 7 member torus, 7 nanometers in diameter 2 nanometer hole. ancestral condition homohexamer or homoheptamer of identical lsm subunits. lsm proteins in eukaryotes form heteroheptamers of 7 different lsm subunits, such sm proteins. binding between lsm proteins best understood eight-strand description of lsm fold. five-strand half of beta sandwich of 1 subunit aligns three-strand half of beta sandwich of adjacent subunit, forming twisted 8-strand beta sheet aβ4a/aβ3b/aβ2a/aβ1/aβ5/bβ4b/bβ3a/bβ2b, , b refer 2 different subunits. in addition hydrogen bonding between aβ5 , bβ4b beta strands of 2 lsm protein subunits, there energetically favorable contacts between hydrophobic amino acid side chains in interior of contact area, , energetically favorable contacts between hydrophilic amino acid side chains around periphery of contact area.

rna oligonucleotide binding

lsm rings form ribonucleoprotein complexes rna oligonucleotides vary in binding strength stable complexes (such sm class snrnps) transient complexes. rna oligonucleotides bind inside hole (lumen) of lsm torus, 1 nucleotide per lsm subunit, additional nucleotide binding sites have been reported @ top (α helix side) of ring. exact chemical nature of binding varies, common motifs include stacking heterocyclic base (often uracil) between planar side chains of 2 amino acids, hydrogen bonding heterocyclic base and/or ribose, , salt bridges phosphate group.