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