Radical SAM Superfamily Workshop!!! John A. Gerlt!!! Enzyme Function Initiative!! September 29, 2012! Why are we here?!

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1 Radical SAM Superfamily Workshop!!! John A. Gerlt!!! Enzyme Function Initiative!! September 29, 2012! Why are we here?!

2 The EFI s first community workshop! EFI/NYSGRC RSS Community Discovery of novel functions is a hard problem: What can the EFI/NYSGRC do for you, and what can you do for us? Why the radical SAM superfamily?! S. J. Booker, Curr Opin Chem Biol 2009

3 Novel radical mechanisms of interest to many! S. J. Booker, Curr Opin Chem Biol 2009 A huge superfamily! InterPro IPR InterPro 64,005 Pfam 44,680 PFam PF04055 SFLD 48,479 Unique Sequences

4 Diverse substrate specificities and reactions! Vast areas of unexplored sequence/function space! Coloured by Reaction Class Numbered by known functions courtesy Squire Booker Clustered at 1 x E-Value

5 The EFI s first community workshop! What can the EFI/NYSGRC do for the RSS community? 1. Tools to enable a genomic enzymology perspective (large-scale) on substrate specificity and mechanism (Patsy, Gemma, and Shoshana) 2. Tools to discover new reactions by predictions of novel substrate specificities (Matt) 3. Tools to analyze genome neighborhood context for function context (in progress) 4. Clones, purified proteins, and structures (Steve) 4. Nucleate multidisciplinary projects to define sequence, structure, and function space in the RSS The EFI s first community workshop! What can the RSS community do for the EFI/NYSGRC? 1. Provide input on what new tools will be necessary to describe and predict substrate specificities and mechanisms in the RSS 2. Provide new test cases for the development of in silico docking protocols for complicated active sites: Fe-S center, 5 -deoxyadenosine radical, control of radical reactions 3. Facilitate the development of large scale protein production and structure determination

6 U54 GM093342: Enzyme Function Initiative (EFI)! bioinformatics x-ray / computation enzymology biology Group 1 Group 2 Group 3! " function! "! " Group 4 Outliers sequence structure reaction function Illinois John Gerlt John Cronan Jonathan Sweedler Texas A&M Frank Raushel UCSF Patricia Babbitt Matthew Jacobson Andrej Sali Brian Shoichet Albert Einstein Steven Almo University of Virginia Wladek Minor Boston University Karen Allen University of New Mexico Debra Dunaway-Mariano University of Utah C. Dale Poulter Vanderbllt University Richard Armstrong EFI: Deliverables! 1. Develop a robust sequence/structure-based strategy for facilitating discovery of in vitro enzymatic and in vivo metabolic/physiological functions of unknown enzymes discovered in genome projects. 2. Disseminate to the community the intellectual, computational, and experimental tools, protocols, materials, and guidelines for determining in vitro and in vivo functions of unknown enzymes. 3. Collaborate with the community to facilitate sequence/superfamily analyses as well as homology modeling and in silico docking of ligand libraries to unknown members of other enzyme superfamilies.

7 EFI s funnel for functional discovery! bioinformatics! MEHRSYW! Target! X-ray/ modeling! docking! enzymology! Structure! S! P! Reaction! genetics! metabolomics! Physiological Function! Bridging Projects that provide targets! Amidohydrolase (Frank Raushel, TAMU): large functionally diverse superfamily, single substrate, single domain Enolase (John Gerlt, UIUC): small functionally diverse superfamily, single substrate, catalytic and specificity domains Glutathione Transferase (Richard Armstrong, Vanderbilt): Large/diverse superfamily, bisubstrate ( always glutathione), small molecule and protein substrates Haloalkanoic Acid Dehalogenase (Karen Allen, BU, and Debra Dunaway-Mariano, UNM): large/diverse superfamily, phosphomonoesterases, catalytic and specificity domains Isoprenoid Synthase (C. Dale Poulter, UU): one (cyclases) or two (isoprenyl transfer) substrates, limited number of substrates, product determined by active site shape

8 Scientific Cores that provide tools! Superfamily/Genome (Patsy Babbitt, UCSF): Sequences and similarity networks, genome context, operons Protein (Steve Almo, AECOM): Gene cloning/synthesis, protein purification, ligand binding Structure (Steve Almo, AECOM): Crystallization and structure determination (50 new structures/year) Computation (Matt Jacobson, Andrej Sali, Brian Shoichet; UCSF): Functional prediction by homology modeling and in silico ligand docking Microbiology (John Cronan and Jonathan Sweedler, UIUC): Genetics, transcriptomics, metabolomics Functional assignment: the old way! - O 2 C O Ala N H H L-Ala-L-Glu CO 2 - AE Epim - O 2 C O H NH Ala CO 2 - L-Ala-D-Glu

9 Functional assignment: a better way! H2N NH2+ H2N HN CO2- O H NSAR NH2+ HN NH NH -O C 2 N-Succ-L-Arg H -O C 2 N-Succ-D-Arg Prediction! Crystal! Functional assignment: how we do it now!! 2PMQ SNF from PSI-2 CO2- O

10 Genome context of 2PMQ: multiple docking targets! (Pelagibaca bermudensis)! Kinetics with Pro/4-OH Pro betaines! Roseovarius sp. HTCC2601! (2PMQ)! k cat [s -1 ]! K M [mm]! k cat /K M [M -1 s -1 ]! Pro-betaine! 5.1 ± 0.06! 13 ± 3! 380! Hyp-betaine! 240 ± 100! 56 ± 30! 4300! H N + CO 2 - OH - O 2 C H N + OH

11 Pathway for 4-OH ProB utilization! N + COO - OH 2PMQ N + COO - Rieske! (demethylase)! OH COO - demethylase! N OH 4-OH L-Pro betaine 4-OH D-Pro betaine H 2 N + COO - OH D-amino acid! oxidase! N COO - OH NH 2 OH O COO - DHDPS " 4-OH D-Pro H O O COO - DH! (NAD + )! - O O O COO -!-ketoglutarate EFI: Deliverables! 1. Develop a robust sequence/structure-based strategy for facilitating discovery of in vitro enzymatic and in vivo metabolic/physiological functions of unknown enzymes discovered in genome projects. 2. Disseminate to the community the intellectual, computational, and experimental tools, protocols, materials, and guidelines for determining in vitro and in vivo functions of unknown enzymes. 3. Collaborate with the community to facilitate sequence/superfamily analyses as well as homology modeling and in silico docking of ligand libraries to unknown members of other enzyme superfamilies.

12 Deliverables to the RSS Community! 1. Develop a robust sequence/structure-based strategy for facilitating discovery of in vitro enzymatic and in vivo metabolic/physiological functions of unknown enzymes discovered in genome projects. 2. Disseminate to the community the intellectual, computational, and experimental tools, protocols, materials, and guidelines for determining in vitro and in vivo functions of unknown enzymes. 3. Collaborate with the community to facilitate sequence/superfamily analyses as well as homology modeling and in silico docking of ligand libraries to unknown members of other enzyme superfamilies. Large scale capabilities that can be shared! Superfamily/Genome (Patsy Babbitt, UCSF): Sequences and similarity networks, genome context, operons Protein (Steve Almo, AECOM): Gene cloning/synthesis, protein purification, ligand binding Structure (Steve Almo, AECOM): Crystallization and structure determination (50 new structures/year) Computation (Matt Jacobson, Andrej Sali, Brian Shoichet; UCSF): Functional prediction by homology modeling and in silico ligand docking Microbiology (John Cronan and Jonathan Sweedler, UIUC): Genetics, transcriptomics, metabolomics

13 From the EFI! Superfamily/Genome (Patsy Babbitt, UCSF): Sequences and similarity networks, genome context, operons Protein (Steve Almo, AECOM): Gene cloning/synthesis, protein purification, ligand binding Structure (Steve Almo, AECOM): Crystallization and structure determination (50 new structures/year) Computation (Matt Jacobson, Andrej Sali, Brian Shoichet; UCSF): Functional prediction by homology modeling and in silico ligand docking Microbiology (John Cronan and Jonathan Sweedler, UIUC): Genetics, transcriptomics, metabolomics From the NYSGRC! Superfamily/Genome (Patsy Babbitt, UCSF): Sequences and similarity networks, genome context, operons Protein (Steve Almo, AECOM): Gene cloning/synthesis, protein purification, ligand binding Structure (Steve Almo, AECOM): Crystallization and structure determination (50 new structures/year) Computation (Matt Jacobson, Andrej Sali, Brian Shoichet; UCSF): Functional prediction by homology modeling and in silico ligand docking Microbiology (John Cronan and Jonathan Sweedler, UIUC): Genetics, transcriptomics, metabolomics

14 Possible outcomes from the workshop! 1. Use tools now available from the EFI and clones from NYSGRC to enhance the breadth and depth of your science. 2. Provide input to the EFI for developing additional sequence/ genome neighborhood/computational tools. 3. Collaborate with the NYSGRC to develop higher throughput strategies for anaerobic protein production and structure determination. 4. Collaborate with the EFI and NYSGRC to facilitate new focused projects for discovering novel functions. 5. Nucleation of new large scale (multidisciplinary) projects focused on exploring sequence/function/structure diversity. Access to Workshop Materials From EFI Website! enzymefunction.org!

15 Access to Workshop Materials From EFI Website! enzymefunction.org/resources/workshops! Access to Workshop Materials From SFLD! Go to Radical SAM Superfamily

16 Access to Workshop Materials From SFLD! (Radical SAM Workshop Materials)