Enzyme Structure and Function

Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ

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.

The single-particle structures of a Bacterial Cyanide Dihydratase and a Fungal Cyanide Hydratase

The paper presents high-resolution cryo-EM structures of a bacterial and fungal cyanide-degrading enzyme, revealing structural features and potential reaction mechanisms.

Isoleucine binding and regulation of Escherichia coli and Staphylococcus aureus threonine dehydratase (IlvA)

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

Expression, Purification, and Crystallization of Recombinant Human ABL-1 Kinase for Structure-Based Drug Screening Applications

This paper describes the expression, purification, and crystallization of recombinant human ABL-1 kinase for structural analysis and drug screening in CML.

Burkholderia pseudomallei rubrerythrin promiscuously binds metals in a structurally pre-formed bimetallic binding site

This study investigates metal binding in Burkholderia pseudomallei rubrerythrin using X-ray crystallography and spectroscopy, revealing promiscuous metal binding and pre-formed binding sites.

The Na+-pumping mechanism driven by redox reactions in the NADH-quinone oxidoreductase from Vibrio cholerae relies on dynamic conformational changes

This study identifies five conformational states of Na+-NQR in Vibrio cholerae using mutants and inhibitors, revealing that 2Fe-2S reduction drives Na+ translocation through structural rearrangements.

Cis-nonPro Peptides: Genuine Occurrences and their Functional Roles

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.

Fragment Screening by Weak Affinity Chromatography Identifies Ligands for Neisseria gonorrhoeae Undecaprenyl Diphosphate Synthase

This study identifies ligands for Neisseria gonorrhoeae UPPS using weak affinity chromatography and crystallography, revealing binding sites and structural insights for drug development.

SKiD: A Structure-Oriented Kinetics Database of Enzyme-Substrate Interactions

This paper introduces SKiD, a database linking enzyme kinetics parameters with 3D structural data of enzyme-substrate complexes, enhancing understanding of enzymatic function.

Structural enzymological studies of the long chain fatty acyl-CoA synthetase FadD5 from the mce1 operon of Mycobacterium tuberculosis

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.

Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study.

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.

cctbx.xfel: a suite for processing serial crystallographic data

The paper introduces cctbx.xfel, a suite for processing serial crystallographic data, enabling real-time analysis and merging of diffraction images from synchrotrons and XFELs.

A mutation at the dimer interface regulates catalysis

This study shows that subtle mutations at the dimer interface of FAcD affect enzyme activity by disrupting hydrogen-bonding networks and altering dimer stability.

Structure and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii

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

Structural basis for phosphatidylcholine synthesis by bacterial phospholipid N-methyltransferases

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

Crystal structures of forty- and seventy-one-substitution variants of hydroxynitrile lyase from rubber tree

The paper describes the creation and structural analysis of HbHNL variants with 40 and 71 mutations to resemble SABP2, showing increased structural similarity to SABP2 with more mutations.

Ligand Screening and Discovery using Cocktail Soakingand Automated MicroED

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.

Structure of dimerized assimilatory NADPH-dependent sulfite reductase reveals the minimal interface for diflavin reductase binding

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.

A structural perspective on the temperature-dependent activity of enzymes

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.

Structure of mycobacterial NDH-2 bound to a 2-mercapto-quinazolinone inhibitor

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

Restoration of 3-D structure of insect flight muscle from a rotationally averaged 2-D X-ray diffraction pattern

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

PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank

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

Structure Characterization of Bacterial Microcompartment Shells via X-ray Scattering and Coordinate Modeling: Evidence for adventitious capture of cytoplasmic proteins

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.

Functional and phylogenomic approaches reveal novel types of M42 peptidases with contrasted enzymatic properties in Archaea

The paper identifies and classifies novel M42 peptidases in Archaea, revealing their functional diversity and evolutionary history through phylogenomic and structural analyses.

Crystal structure of a thermophilic family II inorganic pyrophosphatase enabling high-temperature adaptation in Thermodesulfobacterium commune

This study characterizes the crystal structure of a thermophilic family II inorganic pyrophosphatase from Thermodesulfobacterium commune, revealing structural features that confer thermal stability.

Ambient temperature structural studies of Penicillin-binding Protein 2a of Methicillin-Resistant Staphylococcus aureus with XFELs and synchrotrons

This study presents room-temperature structures of PBP2a using SFX to reveal dynamic features and conformational changes relevant to antibiotic resistance.

PDBCleanV2: A Python Library for Generating Consistent Structure Datasets

PDBCleanV2 generates consistent structure datasets by standardizing labeling, chain names, and numbering for protein structures.

Massive Compression for High Data Rate Macromolecular Crystallography (HDRMX): Impact on Diffraction Data and Subsequent Structural Analysis

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

Heterologous production, purification and crystallization of 24C-sterol methyltransferase from Candida albicans

This study produces, purifies, and crystallizes 24C-sterol methyltransferase from Candida albicans to support future crystallographic studies.

Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum

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.