Dr. Yonca Yuzugullu PERG (Protein Engineering Research Group)
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1 Dr. Yonca Yuzugullu PERG (Protein Engineering Research Group) BSc, 1997 Ankara University, Turkey PhD, 2010 Middle East Technical University, Turkey Lecturer in Department of Biology Kocaeli University, Turkey
2 Understanding the oxidative mechanism of catalase from S. thermophilum Yonca Yuzugullu a, Chi Trinh b, Mark Smith b,c, Arwen Pearson b,d, Zumrut B. Ogel e, Melis Zengin a, Michael J. McPherson b a Department of Biological Sciences, Kocaeli University, Turkey, b Astbury Centre for Structural Molecular Biology, University of Leeds, UK, c NATRUE, Brussel, Belgium, d Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg, Germany, e Food Engineering Department, Middle East Technical University, Turkey
3 Catalases One of the most studied class of enzymes Ubiquity of enzyme, its ease of assay (cheap, readily available substrate-h 2 O 2 ) make it an attractive target for molecular biologists and biochemists Reaction : 2 H 2 O 2 2 H 2 O + O 2 (1) Enz (Por Fe III ) + H 2 O 2 Cpd I (Por + Fe IV =O) + H 2 O (2) Cpd I (Por + Fe IV =O) + H 2 O 2 Enz (Por Fe III ) + H 2 O + O 2 (3) 1)Chelikani P, Fita I and Loewen PC. CMLS, Cell. Mol. Life Sci. 61: (2004) 2) Swatala J and Loewen PC. ABB, Arch. Biochem. Biophys. 401: (2002)
4 Classification of Catalases Catalases Monofunctional Catalases Catalase- Peroxidases Mn-Catalases Minor catalases 1)Chelikani P, Fita I and Loewen PC. CMLS, Cell. Mol. Life Sci. 61: (2004) 2)Nicholls P, Fita I and Loewen PC. Adv. Org. Chem. 51 (2001) 3)Swatala J and Loewen PC. ABB, Arch. Biochem. Biophys. 401: (2002)
5 Monofunctional Catalases Have large (75-84 kda) or small (55-69 kda) subunits Tetramer Have strong absorbance in Soret band (406 nm) with Rz (A406/A280) values around 1 Haem b (A) Haem d (B) 1)Chelikani P, Fita I and Loewen PC. CMLS, Cell. Mol. Life Sci. 61: (2004) 2)Loewen PC.Cold Spring Harbor Laboratory Pres: (1997) 3)Nicholls P, Fita I and Loewen PC. Adv. Org. Chem. 51 (2001)
6 Monofunctional Catalases
7 S. thermophilum Catalase Capable of degrading H 2 O 2 (catalase activity) and also oxidize o-diphenolic compounds (phenol oxidase activity) in the absence of hydrogen peroxidase. Tetrameric heme containing protein Catalase and phenol oxidase activities ph 7 1 x heme d / monomer 1) Yuzugullu Y, Trinh CH, Smith MA, Pearson AR, Phillips SEV, Sutay Kocabas D, Bakir U, Ogel ZB, McPherson MJ. Acta Cryst. D69: (2013). 2) Yuzugullu Y, Trinh CH, Fairhurst L, Ogel ZB, McPherson MJ, Pearson AR. Acta Cryst. F69: (2013).
8 CATPO Monomer, PDB Code: 4AUM (Subunit A) View of chain A of PVC (PDB Code: 2IUF) and HPII (PDB Code: 1GGE) superposed onto the CATPO (PDB Code: 4AUM). Gray (CATPO), Magenta (PVC), and Lightteal (HPII) Yuzugullu Y, Trinh CH, Smith MA, Pearson AR, Phillips SEV, Sutay Kocabas D, Bakir U, Ogel ZB, McPherson MJ. Acta Cryst. D69: (2013).
9 The haem is coloured green, Tyr369 magenta, His82 grey, Asn155 purple/blue, Val123 red, Phe160 lemon, Phe161 yellow and Phe168 orange. Yuzugullu Y, Trinh CH, Smith MA, Pearson AR, Phillips SEV, Sutay Kocabas D, Bakir U, Ogel ZB, McPherson MJ. Acta Cryst. D69: (2013).
10 Yuzugullu Y, Trinh CH, Fairhurst L, Ogel ZB, McPherson MJ, Pearson AR. Acta Cryst. F69: (2013).
11 1) Yuzugullu Y, Trinh CH, Smith MA, Pearson AR, Phillips SEV, Sutay Kocabas D, Bakir U, Ogel ZB, McPherson MJ. Acta Cryst. D69: (2013).
12 1) Yuzugullu Y, Trinh CH, Smith MA, Pearson AR, Phillips SEV, Sutay Kocabas D, Bakir U, Ogel ZB, McPherson MJ. Acta Cryst. D69: (2013). 2) Yuzugullu Y, Trinh CH, Fairhurst L, Ogel ZB, McPherson MJ, Pearson AR. Acta Cryst. F69: (2013).
13 The environment of the haem centre of wild-type CATPO (a) and the V123C mutant (b). The 2Fo 2Fc electrondensity map is shown in blue. The covalent bond formed between the S atom of the mutated Cys123 and the C atom of the imidazole ring of His82 is shown. The structure of wild-type CATPO contains haem d, while the V123C variant contains unmodified protohaem (haem b). The proximal ligand of the haem iron, Tyr369, is also illustrated. Yuzugullu Y, Trinh CH, Fairhurst L, Ogel ZB, McPherson MJ, Pearson AR. Acta Cryst. F69: (2013).
14 Yuzugullu Y, Trinh CH, Fairhurst L, Ogel ZB, McPherson MJ, Pearson AR. Acta Cryst. F69: (2013).
15 Questions remain unanswered... How substrate and product flow within the enzyme remain unanswered, particularly related to the oxidase activity. In order to address this, we recently determined the crystal structure of the enzyme-inhibitor complex of CATPO with 3-amino-1,2,4-triazole (3TR) (CATPO- 3TR) at 1.95 Å resolution.
16 Left: The structure of S. thermophilum catalase in complex with 3TR. The haem centre is visible to the left of the panel and the 3TR (shown as sticks with pink carbon atoms) binds in a surface pocket ~12Å from the haem (shown with green carbon atoms). Right: The structure of human catalase (PDB Code; 1DGH) showing the same view of the haem pocket, the conserved catalase fold and the surface site that is occupied by NADP. The top of this site (required to bind the nucleotide moiety is occluded in the S. thermophilum catalase by a loop (left panel, yellow ribbon) explaining the inability of this enzyme to bind NADP.
17 Future Studies Studies to determine the flow of oxidative substrates in active centre of CATPO Further mutagenesis studies to investigate how the product exists Kinetic studies to analyze oxidative substrate specificity of CATPO Studies to determine metal content of CATPO EPR to identify reaction intermediates in catalytic cycle(s) of CATPO
18 Acknowledgements Leeds University Professor Michael J. McPherson Professor Simon Phillips Dr. Chi Trinh University of Hamburg Professor Arwen R. Pearson Middle East Technical University Professor Zümrüt B. Ögel Professor Ufuk Bakır Dr. Didem S. Kocabaş NATRUE Dr. Mark Smith Diamond Işınım Kaynağı
19 POSTER
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