Dr. Matthew Kimber

Understanding the mechanistic details of how proteins recognize, manipulate and modify other molecules requires detailed knowledge of their structures. In my lab, x-ray crystallography is used as the primary tool to probe the molecular architecture of biological objects; the resulting detailed, three-dimensional models provide the context for interpreting established research findings and generating concrete functional hypothesis. These are then tested using further biochemical and biophysical experiments to tease out the critical structure-function relationships. While these approaches are applicable to an enormous range of biological problems, our current work focusses predominantly on bacterial systems, including the mechanisms by which bacteria generate enormous diversity of cell surface polysaccharides, and the architecture and functioning of bacterial microcompartments.

• B.Sc. (Hons) Molecular Genetics and Molecular Cell Biology, University of Toronto, 1993
• Ph.D. Molecular and Medical Genetics, University of Toronto, 2000

Bacterial cell surface polysaccharides

One major program in the lab is concerned with the structural biology underpinning the assembly of bacterial saccharides, with a focus on lipopolysaccharide and capsule. The carbohydrate portions of these molecules are built by glycosyltransferases (GTs), then (sometimes) modified by other enzymes, and transported to the cellular surface. One subset of such modifications we have worked on extensively are termination reactions, where a chemical group (possibly a saccharide, but often a chemical such as phosphomethyl) is added to the distal end of a growing saccharide, preventing further elongation. This modification is in turn required for recognition by the export machinery (wzt-wzm). Our lab is looking at a few variations of this system, trying to understand the diversity of strategies bacteria can employ in such termination events. We are also investigating several O-antigen GTs from different Klebsiella serotypes. An example of this work is our research into the retaining Kdo transferases, WbbB and KpsC. These enzymes catalyze a unique reaction and have a highly unusual structure which is heavily modified from the standard GT template. We also strongly suspect that their reaction mechanism is also unique, and so are working to understand the biochemical details through a combination of structural and enzymological experiments.

Bacterial microcompartments

Bacterial microcompartments are large, icosahedral bodied built from tens of thousands of separate protein chains. Microcompartments have a thin outer shell, and an interior core made of enzymes (and organizing proteins) that produce, and then consume, some sort of volatile and/or toxic intermediate, generally a small aldehyde. One of their interesting features is that the shells are impermeable to enzyme co-factors, so the encapsulated enzyme set needs to recycle cofactors internally. One very important subtype we have been working on is the cyanobacterial b-carboxysomes; carboxysomes catalyse the critical reaction that incorporates atmospheric CO₂ into nascent sugars. Among other work we have determined shell protein structures, determined the structure of both carbonic anhydrases that are encapsulated, and shown that the mechanism of RubisCO recruitment operates differently than assumed. We have also showed that changes in the redox state that occurs once the carboxysomes is complete acts as an “on” switch for encapsulated enzymes. More recently, we have also been working to characterize a catabolic microcompartment of unknown function found mostly in Actinobacteria. We determined structures for all of the shell proteins and most of the enzymes, and shown that the enzymes together comprise an aminoacetone degradation pathway. Ultimately we aim to understand how hundreds of thousands of individual protein chains can interact in a sufficiently controlled manner that an essentially identical object is produced each time.

2019:

• The small RbcS-like domains of the β-carboxysome structural protein, CcmM, bind RubisCO at a site distinct from that binding the RbcS subunit.
  Ryan P, Forrester TJB, Wroblewski C, Kenney TMG, Kitova EN, Klassen JS, Kimber MS.
  J Biol Chem. 2018. doi: 10.1074/jbc.RA118.006330.

2018:

• Structural and kinetic characterization of (S)-1-amino-2-propanol kinase from the aminoacetone utilization microcompartment of Mycobacterium smegmatis.
  Mallette E, Kimber MS. J Biol Chem. 2018 Dec 21;293(51):19909-19918.
• Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis.
  Mallette E, Kimber MS. Biochemistry. 2018 Jul 3;57(26):3780-3789.

2017:

• Single polysaccharide assembly protein that integrates polymerization, termination, and chain-length quality control.
  Williams DM, Ovchinnikova OG, Koizumi A, Mainprize IL, Kimber MS, Lowary TL, Whitfield C.
  Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1215-E1223.
• A Complete Structural Inventory of the Mycobacterial Microcompartment Shell Proteins Constrains Models of Global Architecture and Transport.
  Mallette E, Kimber MS. J Biol Chem. 2017 Jan 27;292(4):1197-1210.

2016:

• McGurn LD, Moazami-Goudarzi M, White SA, Suwal T, Brar B, Tang JQ, Espie GS, Kimber MS.
  The structure, kinetics and interactions of the β-carboxysomal β-carbonic anhydrase, CcaA.
  Biochem J. 2016 Dec 15;473(24):4559-4572.
• Biochemical characterization of bifunctional 3-deoxy-β-D-manno-oct-2-ulosonic acid (β‑Kdo) transferase KpsC from Escherichia coli involved in capsule biosynthesis.
  Ovchinnikova OG, Doyle L, Huang BS, Kimber MS, Lowary TL, Whitfield C.
  J Biol Chem. 2016 Oct 7;291(41):21519-21530.
• Bacterial β-Kdo glycosyltransferases represent a new glycosyltransferase family (GT99).
  Ovchinnikova OG, Mallette E, Koizumi A, Lowary TL, Kimber MS, Whitfield C.
  Proc Natl Acad Sci U S A. 2016;113(22):E3120-9.
• Structure and Mutational Analyses of Escherichia coli ZapD Reveal Charged Residues Involved in FtsZ Filament Bundling.
  Roach EJ, Wroblewski C, Seidel L, Berezuk AM, Brewer D, Kimber MS, Khursigara CM.
  J Bacteriol. 2016;198(11):1683-93.
• The Klebsiella pneumoniae O12 ATP-binding Cassette (ABC) Transporter Recognizes the Terminal Residue of Its O-antigen Polysaccharide Substrate.
  Mann E, Mallette E, Clarke BR, Kimber MS, Whitfield C. J Biol Chem. 2016; 291(18):9748-61.
• Structural and Kinetic Characterization of the 4-Carboxy-2-hydroxymuconate Hydratase from the Gallate and Protocatechuate 4,5-Cleavage Pathways of Pseudomonas putida KT2440.
  Mazurkewich S, Brott AS, Kimber MS, Seah SY. J Biol Chem. 2016;291(14):7669-86.

2015:

• YehZYXW of Escherichia coli Is a Low-Affinity, Non-Osmoregulatory Betaine-Specific ABC Transporter.
  Lang S, Cressatti M, Mendoza KE, Coumoundouros CN, Plater SM, Culham DE, Kimber MS, Wood JM. Biochemistry. 2015; 54(37):5735-47.
• Structures, Functions, and Interactions of ClpT1 and ClpT2 in the Clp Protease System of Arabidopsis Chloroplasts.
  Kim J, Kimber MS, Nishimura K, Friso G, Schultz L, Ponnala L, van Wijk KJ.
  Plant Cell. 2015;27(5):1477-96.

2014:

• Crystal Structure and Site-directed Mutational Analysis Reveals Key Residues Involved in Escherichia coli ZapA Function
  Roach EJ, Kimber MS, Khursigara CM. J Biol Chem. 2014; 289(34):23276-86.
• Interactions and structural variability of β-carboxysomal shell protein CcmL
  Keeling TJ, Samborska B, Demers RW, Kimber MS. Photosynth Res. 2014; 121(2-3):125-33

2013:

• Identification and characterization a carboxysomal γ-carbonic anhydrase from the cyanobacterium Nostoc sp. PCC 7120
  de Araujo C, Arefeen D, Tadesse Y, Long BM, Price GD, Rowlett RS, Kimber MS, Espie GS.
  Photosynth Res. 2014; 121(2-3):133-50
• The UDP-glucose Dehydrogenase of Escherichia coli K-12 Displays Substrate Inhibition by NAD That Is Relieved by Nucleotide Triphosphates.
  Mainprize IL, Bean JD, Bouwman C, Kimber MS, Whitfield C.
  J Biol Chem. 2013; 288(32):23064-74
• Characterization of an Aldolase-dehydrogenase complex from the cholesterol degradation pathway of Mycobacterium tuberculosis.
  Carere J, McKenna SE, Kimber MS, Seah SY. Biochemistry. 2013; 52(20):3502–3511

2012:

• A dodecameric CcmK2 structure suggests b-carboxysomal shell facets have a double-layered organization.
  Samborska B and Kimber MS. Structure. 2012; 20(8):1353-62.

2011 and earlier:

• Carboxysomes: cyanobacterial RubisCO comes in small packages.
  Espie GS, Kimber MS. Photosynth. Res. 2011;109(1-3):7-20.
• Structural and theoretical studies indicate that the cylindrical protease ClpP samples extended and compact conformations
  Kimber MS, Yu AYH, Borg M, Chan HS and Houry WA. Structure. 2010; 18(7):798-808
• Structural basis of the oxidative activation of the carboxysomal g-carbonic anhydrase, CcmM. Peña KL, Castel SE, de Araujo C, Espie GS, Kimber MS. (2010)
  Proc Natl Acad Sci U S A. 107(6):2455-60.
• The structural basis of b-peptide-specific cleavage by the serine protease cyanophycinase.
  Law AM, Lai SW, Tavares J, Kimber MS. (2009) J Mol Biol.;392(2):393-404.
• The crystal structure of Aquifex aeolicus prephenate dehydrogenase reveals the mode of tyrosine inhibition.
  Sun W, Shahinas D, Bonvin J, Hou W, Kimber MS, Turnbull J, Christendat D. (2009)
  J Biol Chem. 284(19):13223-32.
• Biochemical and structural analysis of bacterial O-antigen chain length regulator proteins reveals a conserved quaternary structure.
  Larue K, Kimber MS, Ford R, Whitfield C. (2009). J Biol Chem. 284(11):7395-403.
• Cholix toxin, a novel ADP-ribosylating factor from Vibrio cholerae.
  Jørgensen R, Purdy AE, Fieldhouse RJ, Kimber MS, Bartlett DH, Merrill AR. (2008)
  J Biol Chem. 283(16):10671-8.
• Substrate binding by a bacterial ABC transporter involved in polysaccharide export
  Cuthbertson L, Kimber MS, Whitfield C. (2007)
  Proc Natl Acad Sci U S A. 104(49):19529-34.
• The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation.
  Gribun A, Kimber MS, Ching R, Sprangers R, Fiebig KM, Houry WA. (2005)
  J Biol Chem. 280(16):16185-96.
• The structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Pseudomonas aeruginosa.
  Kimber MS, Martin F, Lu Y, Houston S, Vedadi M, Dharamsi A, Fiebig KM, Schmid M, Rock CO. (2004) J Biol Chem. 279(50):52593-602.
• Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens.
  Kimber MS, Vallee F, Houston S, Necakov A, Skarina T, Evdokimova E, Beasley S, Christendat D, Savchenko A, Arrowsmith CH, Vedadi M, Gerstein M, Edwards AM. (2003)
  Proteins. 51(4):562-8.
• Structural basis for specificity switching of the Src SH2 domain.
  Kimber MS, Nachman J, Cunningham AM, Gish GD, Pawson T, Pai EF. (2000)
  Mol Cell. Jun;5(6):1043-9.
• The active site architecture of Pisum sativum b-carbonic anhydrase is a mirror image of that of a-carbonic anhydrases.
  Kimber MS, Pai EF. (2000) EMBO J. 19(7):1407-18.
• b-carbonic anhydrase from Pisum sativum: crystallization and preliminary X-ray analysis.
  Kimber MS, Coleman JR and Pai EF. Acta Crystallogr D Biol Crystallogr. 2000; 56(7):927-9.
• Insights into substrate binding by D-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus D-lactate dehydrogenase.
  Stoll VS, Kimber MS and Pai EF. Structure. 1996; 4(4):437-47.
• Crystallization of the apo forms of the D-lactate dehydrogenase from Lactobacillus pentosus and Leuconostoc mesenteroides
  Stoll VS, Kimber MS, Macfarlane EL, Eikmanns U, Taguchi H and Pai EF.
  Protein and peptide letters. 1995 (2):435 - 440

• MCB*3560 - Structure and Function in Biochemistry
• MCB*4050 - Protein and Nucleic Acid Structure
• MCB*6370 - Protein Structure and Bioinformatics

Graduate Students:

• Laura Seidel (M.Sc., also Khursigara lab)
• Liam Noseworthy
• Manitabhai Govind
• Shaoqian Zong

Research Associates:

• Dr. Taylor Forrester

Former Lab Members:

• Lana El Osta (M.Sc.)
• Patrick Ryan (M.Sc.)
• Charles Wroblewski (M.Sc.)
• Sean White (M.Sc.)
• Tom Keeling (M.Sc.)
• Bozena Samborska (M.Sc.)
• Kerry Peña (M.Sc.)
• Evan Mallette (Ph.D.)