Enzyme Structure and Function

Structural Basis for DNA Replication and Uracil Repair in Phage A-Family DNA Polymerases

The paper presents cryo-EM structures of phage A-family DNA polymerases fused to a uracil-DNA glycosylase domain, revealing their role in reading dU bases and repairing abasic sites during replication.

Fragment Based Active Site Exploration of Urethane Hydrolases Reveals a Diversity of Urethane Binding Modes

The paper uses fragment-based methods to explore urethanase active sites and identifies diverse binding modes for polyurethane fragments.

TorchRef: An open-source PyTorch Framework for Crystallographic Refinement

TorchRef provides a PyTorch framework for crystallographic refinement, offering GPU acceleration and modular design for developing new refinement protocols.

PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search

PDBe-SIFTS improves residue-level sequence-structure mapping with faster search, better scoring, and accurate alignment, comparable to expert curation.

Ligand binding remodels the oligomeric state and active site of Klebsiella pneumoniae azoreductase

This study investigates the role of Klebsiella pneumoniae azoreductase in azo dye reduction, finding that its activity is lower than expected and suggesting non-enzymatic mechanisms may contribute to azo compound reduction in the gut.

Convergent strategies for nanobody-mediated inhibition of an epoxide hydrolase

The paper identifies two classes of nanobodies that inhibit Cif, an epoxide hydrolase from Pseudomonas aeruginosa, through distinct structural strategies targeting a shared epitope.

Bifunctional Architecture Enables Substrate Catalysis and Channeling in Paracoccus TMAO Demethylase

This study reveals a bifunctional mechanism in TMAO demethylase where HCHO is channeled from a catalytic core to a THF-binding site, linking TMAO demethylation with one-carbon transfer.

Substrate-enhanced filamentation of 3-methylcrotonyl-CoA carboxylase in Legionella pneumophila

The paper presents the cryo-EM structure of Legionella pneumophila's MCC and identifies substrate-induced filamentation, suggesting a role in bacterial life cycle differentiation.

The Structural Basis of Malodorant Skatole Formation by the Glycyl Radical Enzyme Indoleacetate Decarboxylase

This paper determines the structure of indoleacetate decarboxylase and challenges the proposed mechanism of skatole formation by showing it may follow a Kolbe-type decarboxylation rather than hydrogen atom transfer.

Best practices for cryo-trapping time-resolvedcrystallography with the Spitrobot crystal plunger

This paper describes a protocol for cryo-trapping time-resolved crystallography using automated crystal plungers to study enzyme reaction pathways at millisecond resolution.

Structural analysis of Helicobacter pylori glutamate racemase in a monoclinic crystal form

The paper presents a high-resolution crystal structure of Helicobacter pylori glutamate racemase in monoclinic symmetry, highlighting differences in crystal packing due to unit-cell parameter variations.

Discovery and structural analysis of glycoside hydrolase family 176 α-1,2 glucosidase from Arthrobacter humicola A8F5

This paper discovers and structurally analyzes a novel -1,2-glucosidase from Arthrobacter humicola A8F5, revealing its unique mechanism and structural features for cleaving rare -1,2-glucosidic bonds.

Two Glu/Asp Residues Cooperatively Mediate an Early Step of ATP Hydrolysis in GHKL ATPases MutL and GyrB

This study identifies two acidic residues that cooperatively mediate an early step of ATP hydrolysis in GHKL ATPases, refining the catalytic mechanism and linking it to disease-associated variants.

The evolution and mechanistic versatility of the bacterial NADH dehydrogenases type II

This study investigates the evolutionary and mechanistic diversity of bacterial NDH-2s, revealing lineage-specific catalytic mechanisms and their implications for drug development.

Ancestral proteins trace the emergence of substrate specificity and oligomerization within bacterial DEDDy dinucleases

This study reconstructs ancestral bacterial DEDDy dinucleases to trace the evolution of substrate specificity and oligomerization from a dimeric ancestor with intermediate preferences.

Quaternary structures of Streptococcus pneumoniae Nucleoside Diphosphate Kinase: from hexamers to supramolecular assemblies

This study reports the crystal and cryo-EM structures of Streptococcus pneumoniae NDK, revealing its hexameric form and higher-order supramolecular assemblies, and suggests these structures may modulate its function.

Muscle Diffraction at the Life Science X-ray Scattering Beamline

The paper describes methodological advances at the LiX beamline for high-throughput muscle diffraction experiments on human and animal muscle tissues.

Filamentation and proline inhibition of glutamate kinase

This study investigates the filamentation and proline inhibition mechanisms of Escherichia coli glutamate kinase using cryogenic electron microscopy.

Structure of human aldehyde oxidase under tris(2-carboxyethyl)phosphine-reducing conditions

This study shows that using TCEP instead of DTT for crystallizing hAOX1 prevents enzyme inactivation, enabling better crystallographic studies.

Critical amino acid residues in the N-terminal domain of NADPH-dependent assimilatory sulfite reductase flavoprotein mediate octameric assembly

The paper identifies critical amino acid residues in the N-terminal domain of SiRFP that mediate octameric assembly, revealing their role in stabilizing the enzyme's structure.

Molecular Architecture of the human Citrate Synthase-Malate Dehydrogenase 2 metabolon

The paper provides structural evidence for the human Citrate Synthase-Malate Dehydrogenase 2 metabolon and shows its transient nature and non-specific interaction site.

KNexPHENIX: A PHENIX-Based Workflow for Improving Cryo-EM and Crystallographic Structural Models

KNexPHENIX improves structural models from cryo-EM and crystallography by refining them with better stereochemistry while maintaining model-to-map correlation and reducing overfitting.

Visualizing the mechanism of quinol oxidation and inhibition of a bd-type oxidase using cryo-EM

The paper presents cryo-EM structures of Escherichia coli cytochrome bd-I to elucidate its mechanism of quinol oxidation and inhibition, identifying key residues and structural changes involved in catalysis and drug binding.

Drop on fixed target reaction initiation approach for serial and time resolved crystallography

This paper describes a drop on fixed target method for time-resolved serial crystallography, tested with enzymes to improve measurement consistency across facilities.

Structural insights into interdomain interactions in Entamoeba histolytica APS kinase

This study determines the crystal structures of E. histolytica APS kinase and reveals how an additional domain modulates its catalytic activity through dynamic interdomain interactions.

Aromatic residues in mobile regions distal to the active site support the closed conformation of E. coli DXPS

This study investigates how aromatic residues in E. coli DXPS stabilize the closed conformation of the enzyme during catalysis by analyzing mutagenesis effects on conformational dynamics.

Monomer-dimer structural comparison in quinol-dependent nitric oxide reductase reveals a functional basis for superior enzymatic activity in the dimer

The paper compares monomer and dimer structures of NmqNOR to show how dimerization enhances enzymatic activity by stabilizing the active site conformation.

Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase

This study uses cryo-EM to show that substrate and cofactor binding in mycobacterial L-GDH180 induces tertiary and quaternary structural remodeling.

Unique structural and ligand binding properties of the Staphylococcus aureus serine hydrolase FphE

The paper characterizes the structural and ligand-binding properties of Staphylococcus aureus FphE, revealing its unique dimeric structure and substrate engagement mechanisms.

The X-ray crystal structure of BorF, the flavin reductase subunit of a two-component flavin-dependent tryptophan halogenase

The paper determines the X-ray crystal structure of BorF, a flavin reductase, and describes its structural features and interactions with FAD.