PC1 lactamase

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PC1 ß-lactamase
2
Protein Data Bank

• The PDB is a resource which compiles essential
  information about many proteins.
• Go to the PDB website at www.pdb.org.

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PC1 ß-lactamase

• Well be investigating ß-lactamase. Type PC1
  into the search box.
• More than one result is produced
• How should we choose the one we want to look at?
• What does the information given about each mean?
• How do you know?
• Which one do you think we should choose?

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3blm

• Click on 3blm
• Underneath the image of the structure, click on
  ProteinWorkshop.
• Ribbon vs. Atom view
• Color changes
• Label changes

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Our preferred view

• Ribbons
• Colored by compound
• No water molecules visible (for now)

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1, 2 Structure

• Divide into pairs. Each group will investigate
  the following portions of the enzyme.
• Residues 31-100
• Residues 101-170
• Residues 171-240
• Residues 241-290
• First make your residues visible as atoms and
  molecules (visibility tool) As you go, use your
  amino acid reference translate each residues 3
  letter abbreviation into its 1 letter
  abbreviation. Type this your 1 letter list into
  a Powerpoint slide and email it to me. Well
  combine this information in the next slide.
• Use the labeling tool to label your segment by
  residue.
• Prepare to show and tell and to describe the
  geometry of your segment

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1 structure

• Residues 31-100 KELNDLEKKYNAHIGVYALDTKSGKEVKFNS
  DKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIV
• Residues 101-170 AYSPILEKYVGKDITLKALIEASMTYSDNTANN
  KIIKEIGGIKKVKQRLKELGDKVTNPVRYEIELNYYS
• Residues 171-240 PKSKKDTSTPAAFGKTLNKLIANGKLSKENKKF
  LLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYAS
• Residues 241-290 RNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPND
  KLISETAKSVMKEF

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2 structure
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Hydropathicity

• Describes the hydrophillicness / hydrophobicness
  of a protein.
• Two ways
• Change coloring in Protein Workshop
• Input your sequence into a Kyte-Doolittle
  converter (http//www.vivo.colostate.edu/molkit/hy
  dropathy/index.html)
• Do both of these and be prepared to describe your
  segments 2 structure in terms of the result.

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Hydropathicity
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Hydropathicity
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3 structure

• Lets try to group the types of tertiary
  indicators found in your segments
• a-helices 32-40, 69-81, 119-129 , 132-142,
  145-154, 183-194, 201-213, 221-224, 277-287
• ß-sheets (43-50, 56-60, 94-96)
• (230-237, 244-251, 259-256)
• Turns 51-53, 62-63, 91-92, 107-108, 113-114,
  155-156, 166-167, 174-175, 178-179, 194-195,
  218-220, 227-228, 241-242, 253-254, 270-271,
  288-289
• Folds a-helix between domain 1 (ß-sheet 5
  antiparallel strands and 3 a-helices) and domain
  2 (a-helices.)

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3 structure
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4 structure

• With your partner, go back to the pdb mainpage
  for 3blm and try to determine the 4 structure.
• Look to see if there are any ligands. Think
  about what a ligand would be and would mean in
  this context.
• Prepare to justify your conclusions to your
  classmates.

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4 structure

• No 4o structure.
• No ligands.

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Remember what ß-lactams are supposed to do
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What about water in the ß-lactams scenario?

• It is this reaction which ß-lactamases catalyze!

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So what now?

• Youre the drug researcher trying to develop a
  effective ß-lactam
• What considerations should you investigate
  regarding ß-lactamases?
• What traits of the ß-lactams?
• What traits of the ß-lactamases?
• Which are more easily studied?

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References

• Buckwell, S. C. Page, M. I. Longridge, J. L.,
  Hydrolysis of 6-alkyl penicillins catalyzed by
  b-lactamase I from Bacillus cereus and by
  hydroxide ion. Journal of the Chemical Society,
  Perkin Transactions 2 Physical Organic
  Chemistry (1972-1999) 1988, (10), 1809-13.
• Herzberg, O., Refined crystal structure of
  beta- lactamase from Staphylococcus aureus PC1
  at 2.0 A resolution. J Mol Biol 1991, 217, (4),
  701-19.
• 3. www.pdb.org
• 4. Protein Workshop Viewer accessed via
  www.pdb.org