Alpha/Beta structures Barrels, sheets and horseshoes

Common features Parallel  strands are arranged in barrels or sheets Individual  strands are connected by  helices  motif is a building unit

TIM barrel First observed in enzyme Triosephosphate Isomerase

The core of TIM barrel Core is tightly packed with hydrophobic amino acids Three layers of sidechains

Residue distribution in TIM barrel

Unusual exception Methylmalonyl- Coenzyme A mutase has small hydrophilic residues in the inside of barrel Coenzyme A (green) binds in the barrel

TIM barrel as a domain TIM barrel is always associated with enzymatic function Pyruvate kinase

Location of active site in TIM barrels

Double barrels Phosphoribosyl anthranilate (PRA) isomerase and Indoglycerol phosphate (IGP) synthase in E.coli (enzyme catalysing two reactions in the tryptophan biosynthesis)

Barrel 1 Barrel 2 Some other microorganisms have two separate single-barrel proteins Some microorganisms have triple barrel homologous protein, where the third barrel catalyzes still another reaction in Trp synthesis pathway

TIM barrels: example of enzyme evolution There is evidence that new enzymes can evolve by changing the active site of TIM barrel

Both enzymes are TIM barrels with 26% sequence identity

ordinary horseshoe  -horseshoe fold  horseshoe Present in many proteins with completely unrelated functions

Number of  repeats can vary considerably

Hydrophobic core of  horseshoe In between  strands and helices, NOT in the middle of horseshoe Many leucines in conserved positions  horseshoe proteins are called also LRR (leuine rich repeats) proteins

Leucine-rich motif in the horseshoe a- aliphatic amino acid X- any amino acid The motif is strong enough to be used in structure prediction

 open twisted sheet Parallel or mixed  -sheet with  helices on both sides Number of  -strands vary from 4 to 10 Called also Rossman fold Lactate dehydrogenase

Topology In TIM barrels and horseshoe proteins the topology is fixed In open sheets topology can vary a lot TIM Open  sheet

Location of active site in  open twisted sheet

Sandwiches.... mmmm

Protein structure sandwiches Layered molecules, where each layer represents either  or  structure Represents one of “A” levels in CATH classification Most common:  double sandwich  triple sandwich  double sandwich Open  sheets can be considered.....  sandwiches

What’s that? TATA box binding protein (TBP) is a... sandwich That’s right,  double

End of story? No other  proteins? There is a good deal of other  proteins However, most of them have folds with very few representatives, so they will be not discussed here