Enzyme Structure and Function

CAZyme3D provides a database of 3D structures for CAZymes, enabling structural similarity searches to identify distant homology and classify CAZymes hierarchically.

The paper introduces a deep learning tool called Metric Ion Classification (MIC) to classify ions and waters in cryo-EM and x-ray crystallography structures, identifying mismodeled ions in the PDB.

This paper applies information theory to improve the inverse transform of small angle scattering data by defining a Shannon limit that determines resolution and model selection.

This paper determines the structure of Escherichia coli PatZ, revealing its homotetrameric architecture and the role of the regulatory domain in catalytic activity and substrate specificity.

This study compares isoleucine regulation of IlvA in Escherichia coli and Staphylococcus aureus, revealing structural differences in their regulatory domains and feedback mechanisms.

This paper identifies genuine cis-nonPro peptides using high-resolution data and quality filtering, revealing their functional roles in critical biological sites and carbohydrate-binding proteins.

This study characterizes the structural and enzymatic properties of FadD5, a fatty acyl-CoA synthetase from Mycobacterium tuberculosis, showing its preference for long-chain fatty acids and the importance of its C-terminal domain for activity.

This study investigates the quaternary structure of SfC12DO, revealing its ability to form multiple active oligomers under different conditions and highlighting its potential for bioremediation.

This study investigates the catalytic mechanism of methylisocitrate lyase in Coxiella burnetii, identifying key residues and structural changes involved in its function.

The paper determines the crystal structures of bacterial PmtA and identifies key residues involved in substrate specificity and methylation during phosphatidylcholine synthesis.

This study shows that 2-oxoglutarate induces dodecamer assembly of Methanosarcina mazei glutamine synthetase, enhancing its activity through a cooperative mechanism.

This study develops a workflow combining cocktail soaking with automated microED to enable rapid ligand screening and structure determination from microcrystals, validated with known and novel ligand interactions.

The paper determines the 2.78 Å resolution cryo-EM structure of Escherichia coli SiR, revealing the minimal interface for diflavin reductase binding and distinguishing between hemoprotein and ferredoxin partner interactions.

The paper uses multi-temperature X-ray crystallography to show how temperature-dependent structural changes in enzyme complexes affect activity and challenge assumptions of Arrhenius/Eyring model parameters.

The paper determines the structure of mycobacterial NDH-2 bound to an inhibitor using cryo-EM, revealing structural features that could guide inhibitor design.

The paper demonstrates restoring 3-D structure of insect flight muscle from a 2-D X-ray diffraction pattern using phase-retrieval algorithm.

The paper introduces PDBe tools for analysing small molecules in the PDB, enhancing ligand data access, interaction analysis, and functional role identification.

The paper uses SAXS and PDDF to analyze BMC shell structures and enzyme encapsulation in Haliangium ochraceum BMCs expressed in E. coli, showing cytoplasmic protein capture during assembly.

This study identifies remotely located residues and conformational dynamics as regulators of kinetic properties in homologous glutamate dehydrogenases.

The paper evaluates lossy compression methods for high data rate macromolecular crystallography to minimize information loss while maintaining structural analysis quality.

This study reports three high-resolution structures of a broad-spectrum LarA enzyme, revealing substrate binding mode and residues critical for substrate recognition and catalysis.

This study determines the crystal structure of pyruvic oxime dioxygenase (POD) from Alcaligenes faecalis, revealing its catalytic mechanism and structural features involved in heterotrophic nitrification.

This paper describes a scalable microfluidic device for automated X-ray crystallography that enables efficient and damage-free crystal mounting for protein structure analysis.

This study investigates the redox regulation of Mycobacterium tuberculosis cytochrome bd by its disulfide bond and quinone specificity, showing reduced activity upon disulfide reduction and substrate inhibition with menaquinol.

The paper introduces a deep learning method for ligand identification in cryoEM and X-ray density maps, showing it performs as well as existing methods for X-ray data and can be applied to cryoEM data.

This study introduces AXSI for measuring absolute intramolecular distances in proteins, validated against single-molecule FRET, showing its effectiveness under various solution conditions.

This study characterizes the structural and mechanistic properties of EstS1 esterase, revealing its role in degrading phthalate diesters through a bi-bi ping-pong mechanism and covalent substrate binding.

The paper identifies 38 cases of enzymes with different structures but identical functions, analyzing their sequence, structure, and mechanism to support convergent evolution.

The paper investigates IspE kinase homologs from pathogenic bacteria, identifies structural differences affecting inhibitor binding, and highlights a hydrophobic pocket critical for inhibitor specificity in Acinetobacter baumannii.