The Structural Biology Group uses high resolution X-ray crystallography and cryo-electron microscopy to understand the atomic structure of proteins involved in the production of biofuels and bioproducts. Atomic resolution structures, when combined with genomic and biochemical data, can provide a mechanistic understanding of enzyme activity and specificity. JBEI researchers use this information to help optimize enzymes for the production of biofuels and bioproducts, improving activity and modifying substrate specificities and product profiles.
Projects
- Study the structure function relationships of plant cell wall and lignin synthesis enzymes with the Feedstocks Division, and lignin degrading enzymes with the Deconstruction Division
- Structural studies of Polyketides Synthases and other enzymes in collaboration with the Biofuels and Bioproducts Division
- Solve crystal and cryo-EM structures of proteins involved in biomass production, deconstruction, and biofuels/bioproducts production to generate mechanistic understanding and suggest mutations to improve activity and/or specificity.
- Bring computational structure prediction methods to JBEI research.
Featured Media
Insights Into a Crucial Component of Plant Cell Walls
Understanding the Molecular Players Involved in Creating Parts of Plant Cell Walls
Tiny Microbes Could Brew Big Benefits for Green Biomanufacturing
Protein Structures Aren’t Set in Stone
Newly Discovered Bacterial Enzyme Produces Useful Biopolymer
AI-Fueled Software Reveals Accurate Protein Structure Prediction
Study Finds ‘Missing Link’ in the Evolutionary History of Carbon-Fixing Protein Rubisco
Missing Lysine Link Could Improve Plant-Based Nutrition
Study Leads to Firmer Grasp of Biochemical “Reactive Handle”
Sewage Sludge Leads to Biofuels Breakthrough
Crystallization Screen Created by JBEI Scientists Reaches the Market
Finding Diamonds in the Rough
New crystallography finding by JBEI and GLBRC benefits bioenergy industry
JBEI Expert José Henrique Pereira explains how X-ray crystallography is used in biofuels production
New Way to Reduce Plant Lignin Could Lead to Cheaper Biofuels
Berkeley Lab and Joint BioEnergy Institute scientists harness enzyme in effort to cut pretreatment costs
Clearing a Potential Road Block to Bisabolane
Joint BioEnergy Institute Researchers Identify Key Enzyme Structure
Featured Publications
- “The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity.” J. Biol. Chem. (2024)
- “Characterization of lignin degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid (PDC).” J. Biol. Chem. (2024)
- “Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1.” J. Biol. Chem. (2024)
- “Complete integration of carbene-transfer chemistry into biosynthesis,” Nature (2023)
- “Structural and biochemical insight into a modular β-1,4-galactan synthase in plants,” Nature Plants (2023)
- “Putative rhamnogalacturonan-II glycosyltransferase identified through callus gene editing bypasses embryo lethality.” Plant Physiol. (2024)
- “Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics,” Nature Catalysis (2023)
- “Structural plasticity enables evolution and innovation of RuBisCO assemblies,” Sci. Adv. (2022)
- “A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides,” ACS Central Science (2022)
- “Accurate prediction of protein structures and interactions using a three-track neural network,” Science (2021)
- “Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450,” Metabolic Engineering (2021)
- “Novel bacterial clade reveals origin of form I Rubisco,” Nature Plants (2020)
- “An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism,” Nature Communications (2020)
- “Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster,” Biochemistry (2020)
- “Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase,” J. Am. Chem. Soc (2020)
- “Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.” mBio. (2019)
- “Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases.” J Ind Microbiol Biotechnol. (2019)
- “Jungle Express is a versatile repressor system for tight transcriptional control.” Nature Comm. (2018)
- “Engineering glycoside hydrolase stability by the introduction of zinc binding.” Acta Cryst. (2018)
- “Discovery of enzymes for toluene synthesis from anoxic microbial communities.” Nature Chem. Bio. (2018)
- “Employing a biochemical protecting group for a sustainable indigo dyeing strategy.” Nature Chem. Biol. (2018)
- “Reply to Kiser: Dioxygen binding in NOV1 crystal structures.” Proc Natl Acad Sci U S A. (2017)
- “Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes.” PLoS One (2017
- “Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism.” Proc Natl Acad Sci U S A. (2017)
- “X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa.” Acta Cryst F (2017)
- “Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase.” Proc Natl Acad Sci U S A. (2016)
- “Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-aryl Ether Cleavage Pathway from Sphingobium sp SYK-6.” J Biol Chem. (2016)
- “Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima.” J. Struct. Biol. (2010)
- “Exploiting The Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin.” Plant Cell Physiol. (2016)
- “Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin.” J Biol Chem. (2015)
- “Structure of the OsSERK2 leucine-rich repeat extracellular domain.” Acta Cryst (2014)
- “Constructing Tailored Isoprenoid Products by Structure-Guided Modification of Geranylgeranyl Reductase.” Structure (2014)
- “Biochemical and Structural Studies of NADH-Dependent FabG Used to Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions.” Appl Environ Microbiol (2014)
- “From soil to structure: a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis.” J. Biol. Chem (2013)
- “Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.” Acta Crystallogr D Biol Crystallogr (2012)
- “Structure of a Three-Domain Sesquiterpene Synthase: A Prospective Target for Advanced Biofuels Production.” Structure (2011)
- “Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima.” J. Struct. Biol. (2010)
Featured Intellectual Property
- “Berkeley Screen: a set of 96 solutions for general macromolecular crystallization.” J. Appl. Cryst. (2017)