Catalytically active holo Homo sapiens adenosine deaminase I adopts a closed conformation
Homo sapiens adenosine deaminase 1 (HsADA1; UniProt P00813) is an immunologically relevant enzyme with roles in T-cell activation and modulation of adenosine metabolism and signaling. Patients with genetic deficiency in HsADA1 suffer from severe combined immunodeficiency, and HsADA1 is a therapeutic target in hairy cell leukemias. Historically, insights into the catalytic mechanism and the structural attributes of HsADA1 have been derived from studies of its homologs from Bos taurus (BtADA) and Mus musculus (MmADA). Here, the structure of holo HsADA1 is presented, as well as biochemical characterization that confirms its h...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Ma, M.T. Jennings, M.R. Blazeck, J. Lieberman, R.L. Tags: adenosine deaminase 1 closed conformation homologs structural inference research papers Source Type: research
Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA
Disulfide-bond-forming proteins (Dsbs) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide-bond-forming protein A (DsbA) catalyzes the formation of the disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, two fragments, bromophenoxy propanamide (1) and 4-methoxy-N-phenylbenzenesulfonamide (2), were identified that bind to DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. ...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Petit, G.A. Mohanty, B. McMahon, R.M. Nebl, S. Hilko, D.H. Wilde, K.L. Scanlon, M.J. Martin, J.L. Halili, M.A. Tags: DsbA fragments cryptic pocket Burkholderia pseudomallei NMR X-ray crystallography research papers Source Type: research
B-factor accuracy in protein crystal structures
The accuracy of B factors in protein crystal structures has been determined by comparing the same atoms in numerous, independent crystal structures of Gallus gallus lysozyme. Both B-factor absolute differences and normal probability plots indicate that the estimated B-factor errors are quite large, close to 9 Å 2 in ambient-temperature structures and to 6 Å 2 in low-temperature structures, and surprisingly are comparable to values estimated two decades ago. It is well known that B factors are not due to local movements only but reflect several, additional factors from crystal defects, large-scale disorder, diffra...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Carugo, O. Tags: accuracy B factors normal probability plot validation protein crystal structures research papers Source Type: research
Molecular basis of transcriptional repression of anti-CRISPR by anti-CRISPR-associated 2
CRISPR – Cas systems are well known host defense mechanisms that are conserved in bacteria and archaea. To counteract CRISPR – Cas systems, phages and viruses have evolved to possess multiple anti-CRISPR (Acr) proteins that can inhibit the host CRISPR – Cas system via different strategies. The expression of acr genes is controlled by anti-CRISPR-associated (Aca) proteins that bind to an upstream promoter and regulate the expression of acr genes during transcription. Although the role of Aca as a transcriptional repressor has been demonstrated, the mechanism of action of Aca has not been determined. Here, the molec...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Lee, S.Y. Kim, G.E. Park, H.H. Tags: Aca2 adaptive immunity anti-CRISPR-associated 2 – Cas Oceanimonas smirnovii crystal structure research papers Source Type: research
Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts
Room-temperature diffraction methods are highly desirable for dynamic studies of biological macromolecules, since they allow high-resolution structural data to be collected as proteins undergo conformational changes. For crystals grown in lipidic cubic phase (LCP), an extruder is commonly used to pass a stream of microcrystals through the X-ray beam; however, the sample quantities required for this method may be difficult to produce for many membrane proteins. A more sample-efficient environment was created using two layers of low X-ray transmittance polymer films to mount crystals of the archaerhodopsin-3 (AR3) photorecep...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Axford, D. Judge, P.J. Bada Juarez, J.F. Kwan, T.O.C. Birch, J. Vinals, J. Watts, A. Moraes, I. Tags: membrane proteins microbial rhodopsin archaerhodopsin retinal LCP room temperature synchrotron proton transport thin-film sample photoreceptors polymer films lipidic cubic phase research papers Source Type: research
A radical approach to radicals
Nitroxide radicals are characterized by a long-lived spin-unpaired electronic ground state and are strongly sensitive to their chemical surroundings. Combined with electron paramagnetic resonance spectroscopy, these electronic features have led to the widespread application of nitroxide derivatives as spin labels for use in studying protein structure and dynamics. Site-directed spin labelling requires the incorporation of nitroxides into the protein structure, leading to a new protein – ligand molecular model. However, in protein crystallographic refinement nitroxides are highly unusual molecules with an atypical chemica...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Liu, Y. Biczysko, M. Moriarty, N.W. Tags: ligand restraints macromolecular refinement quantum chemistry spin labelling nitroxides chemical radicals research papers Source Type: research
X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure
This study constitutes the first report of such a protein arrangement, which has never previously been seen for any protein or NDPK. Further studies are needed to determine its physiological role. However, it may suggest a paradigm for protein storage reflecting the complex mechanism of action of TcNDPK1. (Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Gomez Barroso, J.A. Miranda, M.R. Pereira, C.A. Garratt, R.C. Aguilar, C.F. Tags: quinary multi-hexameric X-ray structure Trypanosoma cruzi nucleoside diphosphate kinases in vivo protein granules research papers Source Type: research
Best practices for time-resolved serial synchrotron crystallography
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resol...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: Schulz, E.C. Yorke, B.A. Pearson, A.R. Mehrabi, P. Tags: time-resolved crystallography serial crystallography SSX structural enzymology mechanistic structural biology research papers Source Type: research
Implications of AlphaFold2 for crystallographic phasing by molecular replacement
The AlphaFold2 results in the 14th edition of Critical Assessment of Structure Prediction (CASP14) showed that accurate (low root-mean-square deviation) in silico models of protein structure domains are on the horizon, whether or not the protein is related to known structures through high-coverage sequence similarity. As highly accurate models become available, generated by harnessing the power of correlated mutations and deep learning, one of the aspects of structural biology to be impacted will be methods of phasing in crystallography. Here, the data from CASP14 are used to explore the prospects for changes in phasing...
Source: Acta Crystallographica Section D - December 22, 2021 Category: Biochemistry Authors: McCoy, A.J. Sammito, M.D. Read, R.J. Tags: protein structure prediction crystallographic phase problem molecular replacement AlphaFold2 research papers Source Type: research
Submission of structural biology data for review purposes
(Source: Acta Crystallographica Section D)
Source: Acta Crystallographica Section D - December 1, 2021 Category: Biochemistry Authors: Baker, E.N. Bond, C.S. Garman, E.F. Newman, J. Read, R.J. van Raaij, M.J. Tags: structural biology data peer review editorial Source Type: research
Ten things I `hate' about refinement
Macromolecular refinement is an optimization process that aims to produce the most likely macromolecular structural model in the light of experimental data. As such, macromolecular refinement is one of the most complex optimization problems in wide use. Macromolecular refinement programs have to deal with the complex relationship between the parameters of the atomic model and the experimental data, as well as a large number of types of prior knowledge about chemical structure. This paper draws attention to areas of unfinished business in the field of macromolecular refinement. In it, we describe ten refinement topics that ...
Source: Acta Crystallographica Section D - November 30, 2021 Category: Biochemistry Authors: Roversi, P. Tronrud, D.E. Tags: refinement restraints correlations bias research papers Source Type: research
Structural analysis of the sulfatase AmAS from Akkermansia muciniphila
Akkermansia muciniphila, an anaerobic Gram-negative bacterium, is a major intestinal commensal bacterium that can modulate the host immune response. It colonizes the mucosal layer and produces nutrients for the gut mucosa and other commensal bacteria. It is believed that mucin desulfation is the rate-limiting step in the mucin-degradation process, and bacterial sulfatases that carry out mucin desulfation have been well studied. However, little is known about the structural characteristics of A. muciniphila sulfatases. Here, the crystal structure of the premature form of the A. muciniphila sulfatase AmAS was determined. Str...
Source: Acta Crystallographica Section D - November 29, 2021 Category: Biochemistry Authors: Li, C.-C. Tang, X.-Y. Zhu, Y.-B. Song, Y.-J. Zhao, N.-L. Huang, Q. Mou, X.-Y. Luo, G.-H. Liu, T.-G. Tong, A.-P. Tang, H. Bao, R. Tags: Akkermansia muciniphila sulfatases mucins protein structure human gut research papers Source Type: research
Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program
CAB, a recently described automated model-building (AMB) program, has been modified to work effectively with nucleic acids. To this end, several new algorithms have been introduced and the libraries have been updated. To reduce the input average phase error, ligand heavy atoms are now located before starting the CAB interpretation of the electron-density maps. Furthermore, alternative approaches are used depending on whether the ligands belong to the target or to the model chain used in the molecular-replacement step. Robust criteria are then applied to decide whether the AMB model is acceptable or whether it must be modif...
Source: Acta Crystallographica Section D - November 29, 2021 Category: Biochemistry Authors: Cascarano, G.L. Giacovazzo, C. Tags: nucleic acids molecular replacement phase refinement automatic model building CAB research papers Source Type: research
Predicting the performance of automated crystallographic model-building pipelines
Proteins are macromolecules that perform essential biological functions which depend on their three-dimensional structure. Determining this structure involves complex laboratory and computational work. For the computational work, multiple software pipelines have been developed to build models of the protein structure from crystallographic data. Each of these pipelines performs differently depending on the characteristics of the electron-density map received as input. Identifying the best pipeline to use for a protein structure is difficult, as the pipeline performance differs significantly from one protein structure to ano...
Source: Acta Crystallographica Section D - November 29, 2021 Category: Biochemistry Authors: Alharbi, E. Bond, P. Calinescu, R. Cowtan, K. Tags: structure solution model building software prediction automated pipelines research papers Source Type: research
New system for archiving integrative structures
Structures of many complex biological assemblies are increasingly determined using integrative approaches, in which data from multiple experimental methods are combined. A standalone system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. Here, the data standards and software tools that support PDB-Dev are described along with the new and updated components of the PDB-Dev data-collection, processing and archiving infrastructure. Following the FAIR (Findable, Accessible, Interoperable and Reusable) principles, PDB-Dev ensures that the results of integrative structu...
Source: Acta Crystallographica Section D - November 29, 2021 Category: Biochemistry Authors: Vallat, B. Webb, B. Fayazi, M. Voinea, S. Tangmunarunkit, H. Ganesan, S.J. Lawson, C.L. Westbrook, J.D. Kesselman, C. Sali, A. Berman, H.M. Tags: PDB-Dev integrative modeling PDBx/mmCIF IHM-dictionary data standards research papers Source Type: research
