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STRUCTURAL and BIOCHEMICAL STUDIES of Streptococcus Sp

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STRUCTURAL and BIOCHEMICAL STUDIES of Streptococcus Sp STRUCTURAL AND BIOCHEMICAL STUDIES OF Streptococcus sp. α-GLYCEROPHOSPHATE OXIDASE Timothy M. Colussi A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVERSITY SCHOOL OF ARTS AND SCIENCES In Partial Fulfillment of the Requirement for the Degree of DOCTOR OF PHILOSOPHY In the Department of Biochemistry of the Wake Forest University School of Medicine December 2009 Winston-Salem, North Carolina Approved By: Al Claiborne, Ph.D., Advisor ______________________________ Examining Committee: S. Bruce King, Ph.D., Chair ______________________________ Thomas Hollis, Ph.D. ______________________________ Derek Parsonage, Ph.D. ______________________________ W. Todd Lowther, Ph.D. ______________________________ ACKNOWLEDGMENTS First I would like to thank Dr. Al Claiborne for affording me the opportunity to work in his lab. His guidance has been a tremendous help to me over the years and his support has helped me grow as a scientific researcher. He has always been willing to give me the opportunity to share my work with other members of the scientific committee both here at Wake Forest and at meetings elsewhere. He has always been willing to help and offer assistance whenever I might have needed it, both scientifically and otherwise. I would also like to thank Dr. Conn Mallet for teaching me both the theory and practice of x-ray crystallography, and how to open a beer bottle using the desk handles at NSLS. He was instrumental in getting me excited about x-ray crystallography. He has also given me guidance throughout my graduate career, even after leaving Wake Forest University. An enormous thank you to Dr. Derek Parsonage, my molecular biology guru. He patiently answered the same question three times on three different days many times throughout my graduate career involving molecular biology and/or enzyme kinetics. I could not have accomplished much without his continued help. A huge thank you also to Dr. Tom Hollis for his guidance, not only with x-ray crystallography, but other aspects of my graduate career. He never turned me away when I had a question and was always willing to help me figure out the answer to the many questions I had. Thank you to Drs. Bruce King and Todd Lowther for serving on my committee and the advice and guidance you have given me during my graduate career. ii Dr. Andy Karplus was instrumental in the preparing Chapter II of this thesis. I am grateful for the time he took helping me with structure refinement and figure preparation even though he was three time zones away. I would also like to thank the former members of the Claiborne lab: Conn Mallet, Derek Parsonage, Jamie Wallen, Nate Nicely, Bill Boles, Carleitta Paige, and Sumana Choudhury. You were always willing to help when I needed it. I would also like to thank the many friends I have met through graduate school over the years. I will miss all the great times we have shared together having fun and complaining about the recent Wake Forest defeat in either football or basketball, we all know there were many. I will never forget the times you have helped keep me sane when I was about to lose my mind. We all know those times were many, as well. I would also like to thank my family and friends who have supported me through this whole process. I would especially like to thank my mother, Norma Colussi. She is possibly the strongest woman I know and has helped me keep going during any of the tough times I’ve had over the years, even when she didn’t know it. And last but not least, I would like to thank the man for whom I dedicate this to, my father, Larry Colussi. He is my hero and the reason I am the way I am today. This one’s for you Dad. iii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ......................................................................................... ii LIST OF ABBREVIATIONS .................................................................................... v LIST OF ILLUSTRATIONS ..................................................................................... vi ABSTRACT ............................................................................................................... ix Chapter I. INTRODUCTION: FLAVOPROTEIN OXIDASES, DEHYDROGENASES, AND α-GLYCEROPHOSPHATE BIOLOGY.......................................................................................... 1 II. STRUCTURE OF α-GLYCEROPHOSPHATE OXIDASE FROM Streptococcus sp.: A TEMPLATE FOR THE MITOCHONDRIAL α-GLYCEROPHOSPHATE DEHYDROGENASE ......................... 31 Published in Biochemistry, January 2008 III. KINETIC ANALYSIS OF α-GLYCEROPHOSPHATE OXIDASE FROM Streptococcus sp.: IDENTIFICATION OF RESIDUES IMPORTANT IN GLP-SUBSTRATE BINDING AND CATALYSIS...................................................................................... 78 IV. CONLUSIONS AND FUTURE DIRECTIONS ............................... 112 SCHOLASTIC VITAE .............................................................................................. 126 iv LIST OF ABBREVIATIONS DAAO, D-amino acid oxidase; ThiO, glycine oxidase; MSOX, monomeric sarcosine oxidase; FAD, flavin adenine dinucleotide; PutA, L-proline dehydrogenase; DHOD, dihydroorotate dehydrogenase; P5C, Δ1-pyrroline-5-carboxylate; DHO, dihydroorotate; OA, orotate; NAD, nicotinamide adenine dinucleotide; FMN, flavin mononucleotide; GlpK, glycerol kinase; GlpO, α-glycerophosphate oxidase; GlpF, glycerol facilitator; HPr, histidine phosphocarrier protein; FBP, fructose 1,6-bisphosphate; GlpD, α- glycerophosphate dehydrogenase; Glp, α-glycerophosphate; DHAP, dihydroxyacetone phosphate; GAP, glyceraldehyde phosphate; TIM, triosephosphate isomerase; ATP, adenosine triphosphate; GPD1, cytosolic α-glycerophosphate dehydrogenase; GPD1-L, cytosolic α-glycerophosphate dehydrogenase like protein; mGPD, mitochondrial α- glycerophosphate dehydrogenase; EMT, enzyme-monitored turnover; MAD, multiwavelength anomalous dispersion; SeMet, selenomethionine; MR, molecular replacement; GlpOΔ, α-glycerophosphate oxidase deletion mutant; mitoGlpD, mitochondrial α-glycerophosphate dehydrogenase; bactGlpD, bacterial α- glycerophosphate dehydrogenase; PCR, polymerase chain reaction; EDTA, ethylenediaminetetraacetic acid; PEG, polyethylene glycol; GR, glutathione reductase; ADP, adenosine diphosphate; NAG, N-acetylglycine; D-Ala, D-alanine; Gut2P, yeast mitochondrial α-glycerophosphate dehydrogenase; Cox-1, prostaglandin H2 synthase; HRP, horseradish peroxidase; DTT, dithiothreitol; β-OG, 1-O-n-octyl-β-D- glucopyranoside; PMS, phenazine methosulfate; MTT, 2-(4,5-dimethyl-2-thiazolyl)-3,5- diphenyl-2-H-tetrazolium bromide; SURE, subtilin-regulated gene expression; SDS- PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis v LIST OF ILLUSTRATIONS Schemes Page 1-1 Kinetic mechanism for intact Streptococcus sp. GlpO 22 1-2 Kinetic mechanism for the [Glp] independent reaction seen in the nicked 23 Form of Streptococcus sp. GlpO Tables 1-1 Chemical and spectral differences between flavoprotein oxidases and 3 dehydrogenases. 2-1 Data collection for GlpO and GlpOΔ and phasing statistics for GlpOΔ 40 2-2 Crystallographic refinement statistics for GlpO and GlpOΔ 41 2-3 Steady-state kinetic constants for intact and nicked forms of Streptococcus 44 sp. GlpO and for GlpOΔ 3-1 Results of sulfite titrations of wild-type and mutant GlpOΔ enzymes 93 3-2 Turnover numbers for wild-type and mutant GlpOΔ enzymes from HRP 96 Coupled assay 3-3 Steady-state kinetic constants for GlpOΔ and apparent turnover numbers for 101 GlpOΔ and mutants calculated from enzyme-monitored turnover experiments Figures 1-1 Absorption spectra of glucose oxidase showing different redox states of FAD 5 cofactor 1-2 Sulfite titration from α-glycerophosphate oxidase from Enterococcus 6 casseliflavus 1-3 Spectra of the thiolate and benzoquinoid form of 8-mercaptoflavin 8 1-4 Schematic of a possible carbanion mechanism for the dehydration of 9 α-hyroxyacids 1-5 Depiction of bacterial glycerol metabolism 10 vi 1-6 α-Glycerophosphate shuttle 13 1-7 Sequence alignment of functional GlpOs and GlpDs from bacterial and 16 mitochondrial sources 1-8 Model for triggering host cell inflammation by M. mycoides subsp. mycoides 18 1-9 E. coli and B. halodurans GlpD dimers 20 1-10 Limited proteolysis of Streptococcus sp. and E. casseliflavus GlpO 21 2-1 Dithionite and sulfite titrations of GlpOΔ 45 2-2 Enzyme-monitored turnover of GlpOΔ 46 2-3 Final 2Fo-Fc maps for the FAD redox centers of GlpOΔ, intact GlpO chain A, 49 and intact GlpO chain B 2-4 The GlpOΔ dimer, and superposition of a GlpOΔ monomer with intact GlpO 50 chain A 2-5 Topology diagram for GlpOΔ, and superposition of GlpOΔ domains 1 and 2 52 with a ThiO monomer 2-6 Structure-based sequence alignment for Streptococcus sp. GlpO and four 56 known functional GlpOs and GlpDs from bacterial and mitochondrial sources 2-7 Active-site overlay, in stereo, for GlpOΔ and intact GlpO 60 2-8 Active-site overlay, in stereo, for GlpOΔ, the ThiO-N-acteylglycine (NAG) 62 complex (chain A), and the yeast DAAO-D-Ala complex 2-9 Stereoview of the proposed Glp-binding pocket, including N-acetylglycine 64 (NAG) from ThiO overlay in Figure 8 3-1 Active sites of two structural homologs of Streptococcus sp. GlpO 83 3-2 GlpOΔ active site 84 3-3 Proposed mechanism for Glp-binding, proton abstraction, and hydride 85 transfer for Streptococcus sp. GlpOΔ 3-4 Sulfite titration of the wild-type GlpOΔ 92 3-5 HRP coupled assay for wild-type and mutant GlpOΔ enzymes 95 vii 3-6 Active site overlays, in stereo, of GlpOΔ and E. coli GlpD in complex with 98 phosphate and
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