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JCSG Annual Meeting 2008 The Expanding Protein Universe Mining PSI Structures: JCSG Ligand Server Abhinav Kumar Structure Determination Core.

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Presentation on theme: "JCSG Annual Meeting 2008 The Expanding Protein Universe Mining PSI Structures: JCSG Ligand Server Abhinav Kumar Structure Determination Core."— Presentation transcript:

1 JCSG Annual Meeting 2008 The Expanding Protein Universe Mining PSI Structures: JCSG Ligand Server Abhinav Kumar Structure Determination Core

2 JCSG Annual Meeting 2008 The Expanding Protein Universe Outline Introduction and history Examples of use (live) Statistics Unique ligands Binding mode studies Usage

3 JCSG Annual Meeting 2008 The Expanding Protein Universe Introduction and History Herb’s compilation of JCSG data –Porting Excel sheet to Web server http://smb.slac.stanford.edu/public/jcsg/cgi/jcsg_ligand_check.pl Automating tasks –Andrew’s script to produce the list of PSI structures released by PDB –Script to download the pdbs and extract relevant information »Database for the Ligand server

4 JCSG Annual Meeting 2008 The Expanding Protein Universe Examples of Use

5 JCSG Annual Meeting 2008 The Expanding Protein Universe Live Examples of query entry Executing search Explanation of links in the search results Summary

6 JCSG Annual Meeting 2008 The Expanding Protein Universe Number of Structures and unique Compounds PSI: solid bar JCSG: open bar 288 158 92 27 Distribution of Ligands

7 JCSG Annual Meeting 2008 The Expanding Protein Universe Ligands 67/74 (JCSG) 18/22 (SECSG)

8 JCSG Annual Meeting 2008 The Expanding Protein Universe Co-factors 22 in PSI, 20 in JCSG Organics 22 in PSI, 6 in JCSG

9 JCSG Annual Meeting 2008 The Expanding Protein Universe Ions Metal 24 in PSI,10 in JCSG Non-metal 21 in PSI,12 in JCSG

10 JCSG Annual Meeting 2008 The Expanding Protein Universe Buffers (14,10) Precipitants (13,9) Cryos

11 JCSG Annual Meeting 2008 The Expanding Protein Universe Cryo-protectant agents in JCSG Structures Cryo # of times used # of times observed in structure EDO230179 (77.8 %) GOL21393 (43.7 %) MPD6623 (34.8 %) PEG2005618 (32.0 %) PEG4003510 (28.6 %)

12 JCSG Annual Meeting 2008 The Expanding Protein Universe PFAMs (1292 in PSI, 392 in JCSG) 12 9 6 5 9 10 9 4 7 5 10 11 7 10 13 15 8 6 9 14 11 15 11 14 13 10 18 11 14 18 Number of ligands

13 JCSG Annual Meeting 2008 The Expanding Protein Universe PDB IDLigand NameIDCenter 1KPH, 1KPIDidecyl-Dimethyl-Ammonium10ATBSGC 1X92D-Glycero-D-Mannopyranose-7-PhosphateM7PMCSG 1LW43-Hydroxy-2-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl- Pyridin-4-Ylmethyl)- Amino]-Butyric Acid TLPNYSGXRC 2B4BN-Ethyl-N-[3-(Propylamino)Propyl]Propane- 1,3-DiamineB33NYSGXRC 1O8BBeta-D-Arabinofuranose-5'-PhosphateABFMCSG 1RTW(4-Amino-2-Methylpyrimidin-5-Yl)Methyl Dihydrogen PhosphateMP5NESG 1TUFAzelaic AcidAZ1NYSGXRC 2PUZN-(Iminomethyl)-L-Glutamic AcidNIGNYSGXRC 2OU31h-Indole-3-CarbaldehydeI3AJCSG 2OSU6-Diazenyl-5-Oxo-L-NorleucineDONMCSG 1M333-Hydroxy-Propanoic Acid3OHMCSG 2Q093-[(4s)-2,5-Dioxoimidazolidin-4-Yl]Propanoic AcidDI6NYSGXRC 1N2H, 1N2IPantoyl AdenylatePAJTBSGC 2GVC1-Methyl-1,3-Dihydro-2h-Imidazole-2-ThioneMMZNYSGXRC 1BVRTrans-2-Hexadecenoyl-(N-Acetyl-Cysteamine)- ThioesterTHTTBSGC 1Y80Co-5-MethoxybenzimidazolylcobamideB1MSECSG 2A3LCoformycin 5'-PhosphateCF5CESG 1VR0(2r)-3-Sulfolactic Acid3SLJCSG 2NW96-Fluoro-L-TryptophanFT6NESG 1Y0G2-[(2e,6e,10e,14e,18e,22e,26e)-3,7,11,15,19,23,27,31- Octamethyldotriaconta- 2,6,10,14,18,22,26,30- Octaenyl]Phenol 8PPNYSGXRC 1QPR5-Phosphoribosyl-1-(Beta-Methylene) PyrophosphatePPCTBSGC 1Z2LAllantoate Ion1ALNYSGXRC 1XKL2-Amino-4h-1,3-Benzoxathiin-4-OlSTHNESG 1P445-{[4-(9h-Fluoren-9-Yl)Piperazin-1-Yl]Carbonyl}- 1h-IndoleGEQTBSGC 2OD610-Oxohexadecanoic AcidOHAJCSG Unique Ligands (25) in PSI Structures

14 JCSG Annual Meeting 2008 The Expanding Protein Universe Examples of Unique Ligands (R)-2-Hydroxy-3- Sulfopropanoic acid (3SL) bound to the putative 2-phosphosulfolactatetitle 2 phosphatase from Clostridium Acetobutylicum (1VR0) Indole-3-Carboxaldehyde (I3A) bound to tellurite resistance protein of COG3793 (ZP_00109916.1) from Nostoc Punctiforme PCC 73102 (2OU3) 10-Oxohexadecanoic acid (OHA) bound to Ferredoxin- like protein (JCVI_PEP_1096682647733) from an environmental metagenome (unidentified marine microbe) (2OD6)

15 JCSG Annual Meeting 2008 The Expanding Protein Universe Unknown Ligands (UNL) FB8805A (2Q9K) Protein of unknown functionFK9436A (2OH1) Acetyltransferase Gnat family

16 JCSG Annual Meeting 2008 The Expanding Protein Universe Binding Mode Studies FMN bound in over 340 structures in RCSB Binding mode variation in due to the torsional flexibility in the molecule Several ligands/co-factors bound to the proteins Binding mode studies for co-factors –FMN as an example

17 JCSG Annual Meeting 2008 The Expanding Protein Universe Unique binding modes observed in different PFAM families PFAMPSINon-PSITotal PF01070 FMN-dependent dehydrogenase 088 PF00881 DHOdehase 9817 PF00258 Flavodoxin _1 31316 PF00724 Oxidored._FMN 2810 PF01613 Flavin reductase-like 279 PF01180 Nitroreductase 189 PF01243 Pyridox._oxidase 71421

18 JCSG Annual Meeting 2008 The Expanding Protein Universe PF01070 (FMN-dependent dehydrogenase ) PF00881 (DHOdehase) PF00724 (Oxidored._FMN ) PF00258 (Flavodoxin _1)

19 JCSG Annual Meeting 2008 The Expanding Protein Universe PF01613 (Flavin reductase-like) PF01180 (Nitroreductase) PF01243 (Pyridox._oxidase) 1y30

20 JCSG Annual Meeting 2008 The Expanding Protein Universe PF01264 Two structures of Chorismate Synthase 1qxo, 1um0

21 JCSG Annual Meeting 2008 The Expanding Protein Universe First Structures in PFAMs for Protein-Ligand complexes LigandPFAM (First PDB) ACOPF01121(2F6R) ADPPF01966(2Q14) PF01266(3C4N) PF02641(1O51) PF01637(2FNA) PF00437(1G6O) PF01812(1U3G) PF00265(1XX6) PF00154(1MO3) AMPPF02569(2A7X) PF01687(1T6Y) PF00582(2GM3) PF02254(2G1U) ATPPF02569(2A84) PF01513(1Z0S) PF03328(1U5V) PF06973(2PBZ) PF00582(1MJH) COAPF02522(2NYG) PF02566(2ONF) PF02550(2OAS) PF02629(1Y81) PF02515(1Q6Y) FADPF00743(2GV8) PF04954(2GPJ) PF03486(2GQF) PF01243(2FG9) FMNPF07972(1RLJ) PF08981(1T57) PF04289(2IML) PF03358(1NNI) PF01613(1EJE) GDPPF01996(2PHN) PF03193(1U0L) PF01966(2HEK) HEMPF04261(2IIZ) PF08933(2NWB) NADPF00571(2RC3) PF06408(2PH5) PF01933(2O2Z) PF01958(1J5P) PF01513(1Y3I) PF01467(1EJ2) NAPPF09130(1I36) PF01262(2RIR) PF01408(1ZH8) PF00465(1O2D) PF01513(1Z0U) PF08501(1NVT) PLPPF01168(1CT5) SAHPF01795(1M6Y) PF04445(2OYR) PF02353(1KPG) SAMPF04672(2QE6) PF00590(2NPN) PF01980(2NV4) PF03054(2HMA) PF04013(2QMM) PF02384(2F8L) PF01795(1N2X) PF01555(1G60) PF08241(1P91)

22 JCSG Annual Meeting 2008 The Expanding Protein Universe Page Visits (36 different domains) Tracking since September 2007

23 JCSG Annual Meeting 2008 The Expanding Protein Universe UCSD & Burnham Bioinformatics Core John Wooley Adam Godzik Lukasz Jaroszewski Slawomir Grzechnik Sri Krishna Subramanian Andrew Morse Tamara Astakhova Lian Duan Piotr Kozbial Dana Weekes Natasha Sefcovic Prasad Burra Konstantina Bakolitsa Andrei Istomin Kyle Ellrott Josie Alaoen Cindy Cook GNF & TSRI Crystallomics Core Scott Lesley Mark Knuth Heath Klock Dennis Carlton Thomas Clayton Marc Deller Daniel McMullan Polat Abdubek Julie Feuerhelm Joanna C. Hale Thamara Janaratne Hope Johnson Edward Nigoghossian Linda Okach Sebastian Sudek Glen Spraggon Bernhard Geierstanger Sanjay Agarwalla Anna Grzechnik Connie Chen Dustin Ernst Regina Gorski Sachin Kale Amanda Nopakun Christina Puckett Tiffany Wooten Jessica Canseco Mimmi Brown Scientific Advisory Board Sir Tom Blundell Univ. Cambridge Homme Hellinga Duke University Medical Center James Naismith The Scottish Structural Proteomics Facility Univ. St. Andrews James Paulson Consortium for Functional Glycomics, The Scripps Research Institute Robert Stroud Center for Structure of Membrane Proteins, Membrane Protein Expression Center, UCSF Soichi Wakatsuki Photon Factory, KEK, Japan James Wells UC San Francisco Todd Yeates UCLA-DOE, Inst. for Genomics and Proteomics TSRI, NMR Core Kurt Wüthrich Reto Horst Maggie Johnson Amaranth Chatterjee Michael Geralt Wojtek Augustyniak Pedro Serrano Bill Pedrini Biswaranjan Mohanty Jin-Kyu Rhee TSRI Administrative Core Ian Wilson Marc Elsliger Gye Won Han David Marciano Henry Tien Lisa van Veen Stanford /SSRL Structure Determination Core Keith Hodgson Ashley Deacon Mitchell Miller Herbert Axelrod Hsiu-Ju (Jessica) Chiu Kevin Jin Christopher Rife Qingping Xu Silvya Oommachen Henry van den Bedem Scott Talafuse Ronald Reyes Abhinav Kumar Christine Trame Debanu Das Winnie Lam The JCSG is supported by the NIGMS Protein Structure Initiative Grant U54 GM074898 Ex officio founding members JCSG-1 Raymond Stevens, TSRI Susan Taylor, UCSD Peter Kuhn, SSRL/TSRI Duncan McRee, TSRI/Syrrx Peter Schultz, TSRI/GNF

24 JCSG Annual Meeting 2008 The Expanding Protein Universe Acknowledgements Herb, Andrew, Ashley

25 JCSG Annual Meeting 2008 The Expanding Protein Universe JCSG Annual Meeting 2007

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