Abstract:
:The recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been characterised and its crystal structure elucidated at 1.85A. The global architecture of the protein is reminiscent of that of the amidohydrolase superfamily, consisting of two domains; an (alpha/beta)(8) TIM-like barrel domain, where the catalytic centre is located, and a smaller beta-sheet sandwich domain of unknown function. The c-terminal tails of each subunit extend toward another monomer in a swapping-like manner, creating a hydrogen bond network which suggests its implication in protein oligomerisation. Mutational and structural evidence suggest the involvement of a conserved tyrosine in the reaction mechanism of the enzyme. SmelDhp presents both hydantoinase and dihydropyrimidinase activities, with higher affinity for the natural six-membered ring substrates. For the five-membered ring substrates, affinity was greater for those with aliphatic and apolar groups in the 5th carbon atom, with the highest rates of hydrolysis for d-5-methyl and d-5-ethyl hydantoin (k(cat)/K(m)=2736+/-380 and 944+/-52M(-1)s(-1), respectively). The optimal conditions for the enzyme activity were found to be 60 degrees C of temperature at pH 8.0. SmelDhp retains 95% of its activity after 6-hour preincubation at 60 degrees C. This is the first dihydropyrimidinase used for the hydrolytic opening of non-natural 6-monosubstituted dihydrouracils, which may be exploited for the production of beta-amino acids.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Martínez-Rodríguez S,Martínez-Gómez AI,Clemente-Jiménez JM,Rodríguez-Vico F,García-Ruíz JM,Las Heras-Vázquez FJ,Gavira JAdoi
10.1016/j.jsb.2009.10.013subject
Has Abstractpub_date
2010-02-01 00:00:00pages
200-8issue
2eissn
1047-8477issn
1095-8657pii
S1047-8477(09)00293-7journal_volume
169pub_type
杂志文章abstract::The ability to convert into amyloid fibrils is a common feature of prion proteins. However, not all amyloid-forming proteins act as prions. Here, we compared two homologs of the yeast prion protein Ure2 from Saccharomyces cerevisiae and Saccharomyces paradoxus, ScUre2p and SpUre2p, which have different prion propensit...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.03.008
更新日期:2011-06-01 00:00:00
abstract::Light microscopy (LM) approaches are commonly used to attain a description of the cell structure. Even though LM, if compared to electron microscopy (EM), represents a very fast approach, its resolution is, in principle, much lower than in the case of EM. To improve the LM resolution, computational methods based on re...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00574-9
更新日期:2002-10-01 00:00:00
abstract::OxlT is a bacterial transporter protein with 12 transmembrane segments that belongs to the Major Facilitator Superfamily of transporters. It facilitates the exchange of oxalate and formate across the membrane of the Gram-negative bacterium Oxalobacter formigenes. From an electron crystallographic analysis of two-dimen...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2003.09.002
更新日期:2003-12-01 00:00:00
abstract::Using a combination of atomic force, scanning and transmission electron microscopy, we found that avian erythrocytes infected with the avian malaria parasite Plasmodium gallinaceum develop approximately 60 nm wide and approximately 430 nm long furrow-like structures on the surface. Furrows begin to appear during the e...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2008.03.005
更新日期:2008-06-01 00:00:00
abstract::Citropin 1.1 is a basic, highly hydrophobic, 16-amino acid peptide (GLFDVIKKVASVIGGL-NH(2)), displaying wide-spectrum antimicrobial activities. In this paper we describe the synthesis and antimicrobial properties of citropin 1.1 and its 18 analogs constituting mostly truncated fragments of citropin 1.1. Moreover, we e...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2009.07.012
更新日期:2009-11-01 00:00:00
abstract::In COPII mediated vesicle formation, Sec13/Sec31 heterotetramers play a role in organizing the membranes into a spherical vesicle. There they oligomerize into a cage that interacts with the other COPII proteins to direct vesicle formation and concentrate cargo into a bud. In this role they must be flexible to accommod...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.08.016
更新日期:2018-11-01 00:00:00
abstract::In bacteria, the two-component system (TCS) is the most prevalent for sensing and transducing the environmental signals into the cell. In Salmonella, the small basic protein PmrD is found to protect phospho-PmrA and prolong the expression of PmrA-activated genes. In contrast, Escherichia coli PmrD fails to protect pho...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.06.007
更新日期:2010-12-01 00:00:00
abstract::Accurately determining a cryoEM particle's alignment parameters is crucial to high resolution single particle 3-D reconstruction. We developed Multi-Path Simulated Annealing, a Monte-Carlo type of optimization algorithm, for globally aligning the center and orientation of a particle simultaneously. A consistency crite...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.06.009
更新日期:2007-10-01 00:00:00
abstract::The hypothesis that distinct chromatin domains expand and are remodelled differently when they undergo transcription, replication or cell cycle processes is well accepted. The condensation changes by which chromosomes are transformed at the metaphase-interphase transition are especially interesting and therefore exten...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2008.09.002
更新日期:2008-12-01 00:00:00
abstract::Molecular genetic studies with prokaryotic microorganisms reveal that many different molecular processes contribute to the formation of spontaneous mutations. Besides infidelities in DNA replication and the consequences of environmental mutagens, enzyme-mediated DNA rearrangements bring about important, evolutionarily...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1016/1047-8477(90)90064-j
更新日期:1990-07-01 00:00:00
abstract::Hitherto, the packing arrangement of the aquaporin-1 (AQP1) tetramer in 2-dimensional (2-D) crystals (two-sided plane group p42(1)2) was observed to be largely similar (canonical crystal form) despite the difference in the source of the protein, the glycosylation state of the protein, the type of lipids, and the ratio...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2000.4211
更新日期:2000-05-01 00:00:00
abstract::Interferon regulatory factors (IRFs) are transcription factors for interferon-related genes, which manifest both antiviral and tumor-suppressor activities and regulate cell growth in response to DNA damage. For the transcription initiation of the interferon-beta gene, IRFs form a macromolecular assembly bound to the p...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1998.3970
更新日期:1998-01-01 00:00:00
abstract::The fumarate reductase (flavocytochrome c(3)) from Shewanella frigidimarina (formerly S. putrefaciens) NCIMB400 has been crystallized in the space group P2(1), with cell dimensions of a = 45.447 A, b = 92.107 A, c = 78.311 A, and beta = 91.038 degrees and one molecule per asymmetric unit. A native data set has been co...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1999.4139
更新日期:1999-08-01 00:00:00
abstract::Over recent years advances in cryo-electron microscopy for the study of macromolecular structure have resulted in resolutions in the range 10-15 A becoming routine. With this drive for increased resolution comes the need to collect larger datasets, commonly >10,000 particle images. Manual selection of particles from m...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2003.10.024
更新日期:2004-01-01 00:00:00
abstract::Here we report the first crystal structure of a secretory α-glucoside hydrolase isolated from Pseudoalteromonas sp. K8, PspAG97A, which belongs to glycoside hydrolase family 97 and exhibits halophilic property. PspAG97A lacks an acidic surface, that is considered essential for protein stability at high salinity. Inter...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.09.009
更新日期:2016-12-01 00:00:00
abstract::The unsupervised segmentation method proposed in the current study follows the evolutional ability of human vision to extrapolate significant structures in an image. In this work we adopt the perceptual grouping strategy by selecting the spectral clustering framework, which is known to capture perceptual organization ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.10.013
更新日期:2013-12-01 00:00:00
abstract::The ultrastructure of familial amyloid polyneuropathy (FAP) amyloid fibrils was examined with high-resolution electron microscopy and immunolabeling. Sural nerve biopsies from FAP (Met 30) patients as well as control tissues were prepared for thin-section observations. Extracellular spaces in the vicinity of myelinate...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1998.4052
更新日期:1998-12-01 00:00:00
abstract::X-ray imaging offers a new 3-D view into cells. With its ability to penetrate whole hydrated cells it is ideally suited for pairing fluorescence light microscopy and nanoscale X-ray tomography. In this paper, we describe the X-ray optical set-up and the design of the cryo full-field transmission X-ray microscope (TXM)...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.12.023
更新日期:2012-02-01 00:00:00
abstract::PU.1 and IRF-4, members of the Ets and interferon regulatory families of transcription factors, respectively, form a cooperative ternary complex that is implicated in the regulation of B-cell-specific gene expression. A portion of the cooperativity involves interaction between the PU.1 and IRF-4 DNA-binding domains. W...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00514-2
更新日期:2002-07-01 00:00:00
abstract::The QVIEW image-processing software package provides a graphical user interface for interactive and rapid selection of particles from digital electron micrographs. This package was developed to facilitate the selection of elliptical, hydrophobic, and aggregating particles, which present complications for other particl...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1998.4011
更新日期:1998-09-01 00:00:00
abstract::Accurate image alignment is needed for computing three-dimensional reconstructions from transmission electron microscope tilt series. So far, the best results have been obtained by using colloidal gold beads as fiducial markers. If their use has not been possible for some reason, the only option has been the automatic...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2001.4443
更新日期:2001-12-01 00:00:00
abstract::The Caliciviridae is a family of nonenveloped, icosahedral, positive-sense single-stranded RNA viruses. This family of viruses consists of both animal and human pathogens. Adapting human caliciviruses to cell culture has not been successful, whereas some animal caliciviruses, including San Miguel sea lion virus, have ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/s1047-8477(02)00583-x
更新日期:2003-02-01 00:00:00
abstract::We analyzed a tertiary structure of systemin, the first identified polypeptide plant hormone, using two-dimensional NMR spectroscopy. From these data and molecular dynamics calculations we concluded that the peptide can adopt a Z-like-beta-sheet structure, which has previously been found in many specific DNA-binding p...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1995.1026
更新日期:1995-07-01 00:00:00
abstract::AVS (Application Visualization System) is commercially available software for analyzing and viewing data. AVS is primarily used in the physical sciences and engineering, and here we describe the application of AVS for examining three-dimensional density maps generated by electron microscopy and image processing. For t...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1996.0017
更新日期:1996-01-01 00:00:00
abstract::Traditional single particle reconstruction methods use either the Fourier or the delta function basis to represent the particle density map. This paper proposes a more flexible algorithm that adaptively chooses the basis based on the data. Because the basis adapts to the data, the reconstruction resolution and signal-...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.04.012
更新日期:2012-07-01 00:00:00
abstract::A topological localization of epitopes on the surface of the Aa6 subunit of Androctonus australis hemocyanin has been carried out. First, immunocomplex strings composed of native hemocyanin and monoclonal antibodies were examined in the electron microscope and submitted to an image processing by correspondence analysi...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(90)90087-s
更新日期:1990-03-01 00:00:00
abstract::Cryogenic electron microscopy (cryo-EM) and single-particle analysis enables determination of near-atomic resolution structures of biological molecules. However, large computational requirements limit throughput and rapid testing of new image processing tools. We developed PRIME, an algorithm part of the SIMPLE softwa...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.08.005
更新日期:2018-11-01 00:00:00
abstract::The AAA family proteins usually form a hexameric ring structure. The ATP-binding pocket, which is located at the interface of subunits in the hexamer, consists of three functionally important motifs, the Walker A and B motifs, and the second region of homology (SRH). It is well known that Walker A and B motifs mediate...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.03.001
更新日期:2006-10-01 00:00:00
abstract::Chemotactic methyltransferase, CheR catalyse methylation of specific glutamate residues in the cytoplasmic domain of methyl-accepting chemotactic protein receptors (MCPRs). The methylation of MCPRs is essential for the chemical sensing and chemotactic bacterial mobility towards favorable chemicals or away from unfavor...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.08.005
更新日期:2016-12-01 00:00:00
abstract::Although the fundamental steps in Fourier-based image analysis of electron micrographs of helical structures have not changed significantly since the techniques were developed 30 years ago, there have been developments which aid both the analysis itself and the interpretation of results. Increases in computational res...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1996.0027
更新日期:1996-01-01 00:00:00