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Alpha/Beta structures

Alpha/Beta structures. Barrels, sheets and horseshoes. Common features . Parallel b strands are arranged in barrels or sheets Individual b strands are connected by a helices b-a-b motif is a building unit. TIM barrel. First observed in enzyme T riosephosphate I so m erase.

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Alpha/Beta structures

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  1. Alpha/Beta structures Barrels, sheets and horseshoes

  2. Common features • Parallel b strands are arranged in barrels or sheets • Individual b strands are connected by a helices • b-a-b motif is a building unit

  3. TIM barrel First observed in enzyme Triosephosphate Isomerase

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

  5. Residue distribution in TIM barrel

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

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

  8. Location of active site in TIM barrels

  9. Double barrels • Phosphoribosylanthranilate (PRA)isomerase andIndoglycerol phosphate(IGP) synthase inE.coli(enzyme catalysing tworeactions in thetryptophanbiosynthesis)

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

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

  12. Both enzymes are TIM barrels with 26% sequence identity

  13. ordinary horseshoe a/b-horseshoe fold a/b horseshoe Present in many proteins with completely unrelated functions

  14. Number of b-a-b repeats can vary considerably

  15. Hydrophobic core of a/b horseshoe • In between b strands and helices, NOT in the middle of horseshoe • Many leucines in conserved positions • a/b horseshoe proteins are called also LRR (leuine rich repeats) proteins

  16. 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

  17. a/b open twisted sheet • Parallel or mixed b-sheet with a helices on both sides • Number of b-strands vary from 4 to 10 • Called also Rossman fold Lactate dehydrogenase

  18. Topology • In TIM barrels and horseshoe proteins the topology is fixed • In open sheets topology can vary a lot TIM Open a/b sheet

  19. Location of active site in a/b open twisted sheet

  20. Sandwiches.... mmmm

  21. Protein structure sandwiches • Layered molecules, where each layer represents either a or b structure • Represents one of “A” levels in CATH classification • Most common: • a-b double sandwich • a-b-a triple sandwich • b double sandwich • Open a/b sheets can be considered..... • a-b-a sandwiches

  22. What’s that? • TATA box binding protein (TBP) is a ... sandwich • That’s right, a-b double

  23. End of story? No other a/b proteins? • There is a good deal of other a/b proteins • However, most of them have folds with very few representatives, so they will be not discussed here

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