About

Catherine Drennan is a Professor of Biology and Chemistry at MIT, and an Investigator and Professor at the Howard Hughes Medical Institute. Her research involves using X-ray crystallography and cryo-electron microscopy to investigate the structure and function of enzymes that are medically important in environmental remediation. She is particularly interested in metalloprotein biochemistry and the role of conformational change in catalysis. Drennan has received numerous awards, including election to the National Academy of Sciences in 2023, fellowship in the American Society for Biochemistry and Molecular Biology in 2021, and membership in the American Academy of Arts and Sciences in 2020. Her work contributes to understanding enzyme mechanisms, especially those involving metalloenzymes, and her research has advanced knowledge in structural biology related to environmental and medical applications.

Research topics

• Biochemistry
• Chemistry
• Biology
• Computational biology
• Biophysics
• Computer Science
• Stereochemistry
• Physics
• Cell biology
• Crystallography
• Photochemistry

Selected publications

• How a protein repurposes vitamin B12 as a light sensor

  Nature · 2026-02-04

  articleSenior authorCorresponding
  PublisherDOI

• A highly dynamic mononuclear non-heme iron enzyme for the two-step isonitrile biosynthesis

  Nature Communications · 2026-01-26

  articleOpen accessSenior author

  The recent discovery of the isonitrile biosynthetic enzyme ScoE expanded the catalytic repertoire of the Fe(II)/αKG-dependent dioxygenase enzyme family. ScoE synthesizes an isonitrile functional group from a glycyl-fatty acid adduct, with both the isonitrile nitrogen and carbon atoms coming from the glycyl moiety. This challenging chemistry cannot be performed in a single step. Instead, the mechanism appears to require two half reactions, each involving αKG cleavage to generate a highly reactive iron-oxygen species. Here, we report sixteen crystal structures that provide snapshots along the reaction trajectory of Rv0097, a ScoE homolog from Mycobacterium tuberculosis. These structures, which are both of wild-type and Rv0097 variants, include a substrate 3-((carboxymethyl)amino)decanoic acid (CADA)-bound structure, an αKG-bound structure, and a structure with both CADA and αKG bound. These structural data reveal how Rv0097 employs conformational rearrangements to protect the unstable CADA-reaction intermediate that is formed in the first half reaction while swapping out αKG cleavage products for a second molecule of αKG. Additionally, these structures, together with data from site-directed mutagenesis, provide insight into Rv0097's preference for substrates with long alkyl chains, potentially facilitating efforts to re-engineer ScoE/Rv0097 to synthesize isonitrile functional groups on a wider range of small molecules.

  PublisherDOI

• How ATP and dATP reposition class III ribonucleotide reductase cone domains to regulate enzyme activity

  Science Advances · 2025-11-28

  articleOpen accessSenior authorCorresponding

  Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides. In the majority of cases, RNR activity is allosterically regulated by the cellular 2′-deoxyadenosine 5′-triphosphate (dATP)/adenosine 5′-triphosphate (ATP) ratio. To investigate allosteric activity regulation in anaerobic or class III (glycyl radical containing) RNRs, we determine cryo–electron microscopy structures of the class III RNR from Streptococcus thermophilus (StNrdD). We find that StNrdD’s regulatory “cone” domains adopt markedly different conformations depending on whether the activator ATP or the inhibitor dATP is bound and that these different conformations alternatively position an “active site flap” toward the active site (ATP-bound) or away (dATP-bound). In contrast, the position of the glycyl radical domain is unaffected by the cone domain conformations, suggesting that StNrdD activity is regulated through control of substrate binding rather than control of radical transfer. Hydrogen-deuterium exchange mass spectrometry and mutagenesis support the structural findings. In addition, our structural data provide insight into the molecular basis by which ATP and dATP binding lead to the observed differential cone domain conformations.

  PublisherDOI

• Structural basis for anaerobic alkane activation by a multisubunit glycyl radical enzyme

  Proceedings of the National Academy of Sciences · 2025-08-04 · 2 citations

  articleOpen accessSenior authorCorresponding

  X-succinate synthases (XSSs) are glycyl radical enzymes (GREs) that catalyze the addition of hydrocarbons to fumarate via radical chemistry, thereby activating them for microbial metabolism. To date, the only structurally characterized XSS is benzylsuccinate synthase (BSS), which functionalizes toluene. A distinct subclass of XSSs acts on saturated hydrocarbons, which possess much stronger C(sp 3 )–H bonds than toluene, suggesting mechanistic and structural differences from BSS. Here, we use cryogenic electron microscopy to determine the structure of one such enzyme, (1-methylalkyl)succinate synthase (MASS) from Azoarcus strain HxN1, which functionalizes n -alkanes (C6–C8). The structure reveals an asymmetric dimer in which both sides contain a catalytic α-subunit and accessory γ-subunit. One α-subunit also binds two additional subunits, β and δ. The β-subunit binds a [4Fe–4S] cluster and adopts a fold similar to BSSβ. The β-subunit appears to regulate the flexibility of the α-subunit to enable opening of the active site, affording the binding of n -alkane substrates. The δ-subunit, which lacks homology to known GRE subunits, adopts a rubredoxin-like fold that binds a single Fe ion, an architecture not previously reported for GREs. MASSδ occupies the same region of the α-subunit as the activating enzyme (AE) and may regulate the conformational changes required for glycyl radical installation. Structural comparisons between MASS and BSS reveal differences in how fumarate is bound and show amino acid substitutions that could account for the binding of alkanes versus toluene. Together, this structure offers insight into anaerobic alkane activation via fumarate addition.

  PublisherOA PDFDOI

• PexR is a noncanonical regulator of the peroxide stress response in bacteria

  Nucleic Acids Research · 2025-11-26 · 2 citations

  articleOpen access

  Cells combat peroxide stress using peroxiredoxins and catalases. The paradigmatic H2O2-sensing OxyR or PerR transcription regulators typically control their expression in bacteria. Here, we report our discovery of a noncanonical mechanism for H2O2-signaled regulation of peroxiredoxin ahpC and catalase katB genes in Myxococcus xanthus by PexR, an ATP-binding bacterial enhancer binding protein that acts as a dual-function repressor-activator. PexR, a dimer capable of higher-order oligomerization, binds to dyad-symmetry repeats upstream of ahpC and katB, activating their H2O2-induced σ54-dependent expression. Under peroxide stress-free conditions, PexR downregulates housekeeping σA-dependent ahpC expression. Deleting ahpC causes pleiotropy, and synthetic lethality when eliminated with katB or pexR, indicating PexR-mediated co-regulation of AhpC and KatB as critical for normal growth. We show that resting state PexR is autoinhibited by its N-terminal Zn2+/Fe2+-binding GAF (cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA) domain, which senses H2O2 and releases its bound metal to trigger PexR-activated σ54-dependent expression. Our genomic analyses reveal conservation of PexR and its regulatory elements and, likely, mechanism across Myxococcota, frequently co-occurring with OxyR or PerR, showcasing this phylum's remarkable diversity of potential peroxide stress response regulatory mechanisms. Moreover, PexR likely operates in phyla beyond Myxococcota, and its discovery expands the toolkit for genetically encoded H2O2 sensors.

  PublisherDOI

• A 2.8-Å resolution structure of the skatole-producing glycyl radical enzyme Indoleacetate Decarboxylase enabled by new techniques in cryo-EM grid preparation.

  Structural Dynamics · 2025-09-01

  articleOpen accessSenior author

  Nature has devised an array of enzymatic cofactors that enable challenging chemical transformations to occur on a timescale compatible with biological life. Protein-based amino acid radicals are one example of a simple yet powerful radical cofactor capable of catalyzing diverse chemistry. The glycyl radical enzyme (GRE) superfamily is a prominent example of this type of cofactor and the catalytic power it possesses. GREs use a radical housed on the a-carbon of a glycine residue in the active site to perform catalysis in anaerobic environments. The radical- storing glycine residue is housed in the glycyl radical domain (GRD), which is found at the C-terminus of the polypeptide and must undergo a large conformational change to flip out of the active site for radical installation. This radical must be post-translationally installed by a radical S- adenosyl-L-methionine (rSAM) activating enzyme that is specific to each GRE. Therefore, the GRD is intrinsically highly conformationally dynamic. Some GREs employ additional subunits or secondary structures to both cover the active site and contact the GRD, which keeps the enzyme in a closed state. However, additional dynamic subunits and regions can further complicate structural determination. Initial attempts to structurally characterize the GRE Indoleacetate Decarboxylase (IAD) by both X-ray crystallography and cryo-electron microscopy (cryo-EM) resulted in structures with the active site in an open, disordered conformation. The rapid expansion of the cryo-EM field in recent years has provided new tools for sample preparation, data collection, and analysis. The SPT Labtech chameleon is a non-blotting, alternative grid preparation technique that has been demonstrated to ameliorate air-water interface denaturation and enable the capture of low-occupancy oligomeric states. Here, we utilize the chameleon for cryo-EM grid preparation which has enabled the capture of a high-resolution reconstruction of a tetrameric IAD from the gut microbe Olsenella uli to 2.8-Å resolution in a closed, ordered conformation with the substrate indole-3-acetate bound in the active site.

  PublisherOA PDFDOI

• The cobalamin-binding domain of cobalamin-dependent radical S-adenosylmethionine enzymes: Familiarity in unfamiliar places

  Journal of Inorganic Biochemistry · 2025-12-22 · 1 citations

  articleOpen accessSenior authorCorresponding

  Cobalamin (Cbl)-dependent Radical S -adenosylmethionine (RS) enzymes are well known for their use of two powerful cofactors to catalyze chemically challenging reactions, such as methylations on unactivated carbons and phosphorus centers, ring contractions, ring formations, and thioether bond formations. Our repertoire of Cbl-dependent RS enzyme structures has grown since the first solved structure of the oxetanocin A biosynthetic enzyme OxsB in 2017, which has provided insight into the structural basis of catalysis. In particular, the Cbl-binding domains of these RS enzymes have been found to have interesting structural variations that seem to correlate with enzymatic function, at least for the small number of enzymes that have been characterized. In this review, we highlight the recent research about the Cbl cofactor in Cbl-dependent RS enzymes. We compare modes of Cbl binding and demonstrate a previously undetected connection between a subgroup of Cbl-dependent RS enzymes and the corrinoid iron‑sulfur protein (CFeSP) from the Wood-Ljungdahl pathway of reductive acetogenesis. Additionally, we discuss recent mechanistic findings on Cbl-dependent RS enzymes OxsB and its close homolog AlsB, which have not been recently reviewed. As Cbl-dependent RS enzymes are involved in making antiviral and antibiotic compounds, herbicides, and other molecules of value, understanding and manipulating enzyme activity has implications in both medicine and agriculture. The magicians of cobalamin: Cobalamin-dependent radical S -adenosylmethionine enzymes guide the reactivity of cobalt by adjusting the local environment. • Cbl-dependent enzymes control Co reactivity through the local protein environment • Cbl-dependent RS enzymes can be partitioned into 2 distinct structural classes • Ancient corrinoid cofactor binding motif is found in Cbl-dependent RS enzyme • New insights into roles of Cbl in Cbl-dependent RS enzymes

  PublisherDOI

• Mechanistic Investigation of the Class III Ribonucleotide Reductase

  Structural Dynamics · 2025-03-01

  articleOpen accessSenior author

  All organisms use ribonucleotide reductase (RNR) as the sole source for de novo synthesis of deoxyribonucleotides needed for DNA synthesis. Understanding their mechanism of action can provide evidence for the evolution history of life and valuable insights for developing novel antibiotics. The three classes of RNRs are characterized according to the generation of an active-site thiyl radical that initiates radical-dependent catalytic activity. In addition, the three classes utilize different sources of reducing equivalents for ribonucleotide reduction. In class I and II, RNRs acquire the reducing equivalents from the redoxin/thioredoxin reductase/NADPH system, mediated by a pair of conserved cysteines on its C-terminal tail. However, in class III RNRs, the source of the reducing equivalents can vary from formate to thioredoxin and ferredoxin. For example, class III RNR from T. maritima is proposed to obtain the reducing equivalents from thioredoxin/thioredoxin reductase/NADPH, but the C-terminal cysteine pair conserved in class I and II is absent, which therefore requires a large conformational change of the active-site cysteine loop to allow the direct interaction with thioredoxin. Here, we use structural and biochemical techniques to investigate the re-reduction mechanism of T. maritima class III RNR. Our preliminary result suggests a buried active-site cysteine loop in buffered solution, contradicting the previous crystal structures showing a solvent-exposed loop conformation. We will also describe cryo-EM investigation of the T. maritima class III RNR structures and provide insights into the molecular mechanism of class III RNRs.

  PublisherDOI

• Novel insights into the mechanism of long-range radical transfer in class la ribonucleotide reductase by cryogenic-electron microscopy

  Structural Dynamics · 2025-03-01

  articleOpen accessSenior author

  Ribonucleotide reductases catalyze the only known de novo biosynthetic route to deoxyribonucleotides from the corresponding ribonucleotides, making these enzymes attractive antibacterial targets. The active state of the prototypical Escherichia coli class la RNR consists of a heterodimer of two homodimers, α2 and β2, in which the α2 subunit contains the substrate binding sites, specificity sites, and activity regulation sites, and the β2 subunit contains two di-iron cofactors responsible for the initiation of a 32-Å radical transfer pathway that enables substrate turnover. Recent cryogenic-electron microscopy (cryo-EM) work in the Drennan lab has elucidated the active state structure of this enzyme at 3.6-Å resolution, but required the use of a doubly-mutated variant of β2, E52Q/F3Y122-β2, to decrease the rate of subunit dissociation. Additionally, water molecules, which have been suspected to play a role as proton transfer partners along the radical pathway, were not resolvable. We describe here the use of cryoEM and 2′-azido-2′-deoxycytidine-5′-diphosphate, a mechanism-based inhibitor, to trap the active state structure of the wild type Escherichia coli class la RNR. We obtain a 2.6-Å resolution structure, which enables us to model water molecules along the radical transfer pathway and propose a novel mechanism for conformationally-gated radical transfer across the α/β interface. This work therefore provides a basis for understanding the mechanism of conformationally-gated PCET in class la RNRs.

  PublisherDOI

• STRUCTURAL CHARACTERIZATION OF DIIRON-DEPENDENT PLASMANYLETHANOLAMINE DESATURASE (CarF)FROM <i>Myxococcus xanthus</i>

  Structural Dynamics · 2025-03-01

  articleOpen access

  The plasmanylethanolamine desaturase enzyme (EC 1.14.99.19) is an integral membrane protein responsible for the catalytic conversion of alkyl ether phosphatidylethanolamines (AEPEs) to vinyl ether phosphatidylethanolamine (VEPEs)1-3. VEPEs, collectively known as plasmalogens, are glycerophospholipids characterized by a vinyl ether bond at the glycerol sn-1 position1,3. Localized in mammalian brain, heart, and white blood cells, as well as in most mammalian subcellular membranes, these plasmalogens are critical signaling factors against reactive oxygen species (ROS)1,2,4-11. The vinyl ether functional group reacts with ROS which results in the production of secondary chemical messengers that change the lipid bilayer fluidity, inducing carotenoid production which ultimately combats photooxidative stress1,2,4-11. Studies have shown that plasmalogen deficiency is correlated to various human diseases such as digestive tract-related cancer and Alzheimer’s disease2,3. In this study, we use the bacterial membrane protein, CarF from Myxococcus xanthus which is a canonical plasmanylethanolamine desaturase enzyme, to gain insights in this family of membrane proteins. In the literature, CarF’s role and function is well-established and characterized1; however, the structure, as well as the catalytic mechanism of CarF in connection with plasmalogen biogenesis remain elusive. To fill this gap in knowledge, the main goal of this study is to elucidate the structure of CarF through crystallography and cryo-electron microscopy approaches. Toward this goal, we have developed an efficient expression and purification system for CarF in detergent micelles. Consequently, we have incorporated the purified CarF into membrane scaffold proteins (MSPs) nanodiscs to aid the structural determination of CarF through cryo-EM. This work also intends to propose a mechanism on CarF-mediated plasmalogen production. Through the structure and mechanism of function of the protein, we can have a better understanding of plasmalogens, their cellular functions, and their potential pathologies.

  PublisherDOI

Recent grants

• NIH Grant R01GM069857

  NIH · $3.1M · 2019

• Crystallographic Snapshots of Adenosyl Radical Enzymes

  NSF · $648k · 2006–2012

• Metalloenzyme structure, function and assembly

  NIH · $3.4M · 2018–2028

• NIH Grant R01GM065337

  NIH · $1.8M · 2010

• NIH Grant P41RR001646

  NIH · $7.9M · 2013

Frequent coauthors

• Edward J. Brignole

  Massachusetts Institute of Technology

  92 shared

• Sébastien Dementin

  Centre National de la Recherche Scientifique

  49 shared

• Cintyu Wong

  43 shared

• Marco Jost

  Harvard University

  42 shared

• Sean J. Elliott

  Boston University

  42 shared

• Michael A. Funk

  42 shared

• Stephen W. Ragsdale

  University of Michigan–Ann Arbor

  40 shared

• John M. Essigmann

  Center for Environmental Health

  38 shared

Labs

• Catherine Drennan LabPI

Education

• Ph.D., Biological Chemistry

  University of Michigan

  1995

• A.B., Chemistry

  Vassar College

  1985

Awards & honors

• Fellow, American Society for Biochemistry and Molecular Biol…
• Member, American Academy of Arts and Sciences, 2020
• Dorothy Crowfoot Hodgkin Award, Protein Society, 2020
• Margaret MacVicar Faculty Fellow, 2015-2025
• Howard Hughes Medical Institute, HHMI Investigator, 2008