Abstract:
:Dipeptidase 3 (DPEP3) is one of three glycosylphosphatidylinositol-anchored metallopeptidases potentially involved in the hydrolytic metabolism of dipeptides. While its exact biological function is not clear, DPEP3 expression is normally limited to testis, but can be elevated in ovarian cancer. Antibody drug conjugates targeting DPEP3 have shown efficacy in preclinical models with a pyrrolobenzodiazepine conjugate, SC-003, dosed in a phase I clinical trial (NCT02539719). Here we reveal the novel atomic structure of DPEP3 alone and in complex with the SC-003 Fab fragment at 1.8 and 2.8 Å, respectively. The structure of DPEP3/SC-003 Fab complex reveals an eighteen-residue epitope across the DPEP3 dimerization interface distinct from the enzymatic active site. DPEP1 and DPEP3 extracellular domains share a conserved, dimeric TIM (β/α)8-barrel fold, consistent with 49% sequence identity. However, DPEP3 diverges from DPEP1 and DPEP2 in key positions of its active site: a histidine to tyrosine variation at position 269 reduces affinity for the β zinc and may cause substrate steric hindrance, whereas an aspartate to asparagine change at position 359 abolishes activation of the nucleophilic water/hydroxide, resulting in no in vitro activity against a variety of dipeptides and biological substrates (imipenem, leukotriene D4 and cystinyl-bis-glycine). Hence DPEP3, unlike DPEP1 and DPEP2, may require an activating co-factor in vivo or may remain an inactive, degenerate enzyme. This report sheds light on the structural discriminants between active and inactive membrane dipeptidases and provides a benchmark to characterize current and future DPEP3-targeted therapeutic approaches.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Hayashi K,Longenecker KL,Koenig P,Prashar A,Hampl J,Stoll V,Vivona Sdoi
10.1016/j.jsb.2020.107512subject
Has Abstractpub_date
2020-07-01 00:00:00pages
107512issue
1eissn
1047-8477issn
1095-8657pii
S1047-8477(20)30081-2journal_volume
211pub_type
杂志文章abstract::The structures of the compact and swollen southern bean mosaic virus (SBMV) particles have been compared by X-ray diffraction and proton magnetic resonance (PMR). Small-angle X-ray scattering showed that removal of divalent cations at alkaline pH causes the particle diameter to increase from 289Å in the native SBMV by...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2017.06.003
更新日期:2017-12-01 00:00:00
abstract::The first step to understanding brain function is to determine the brain's network structure. We report a three-dimensional analysis of the brain network of the fruit fly Drosophila melanogaster by synchrotron-radiation tomographic microscopy. A skeletonized wire model of the left half of the brain network was built b...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.08.012
更新日期:2013-11-01 00:00:00
abstract::Water-containing biological material cannot withstand the vacuum of the transmission electron microscope. The classical solution to this problem has been to dehydrate chemically fixed biological samples and then embed them in resin. During such treatment, the bacterial nucleoid is especially prone to aggregation, whic...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.jsb.2006.07.007
更新日期:2006-11-01 00:00:00
abstract::Structural analysis of multi-domain protein complexes is a key challenge in current biology and a prerequisite for understanding the molecular basis of essential cellular processes. The use of solution techniques is important for characterizing the quaternary arrangements and dynamics of domains and subunits of these ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.11.004
更新日期:2011-03-01 00:00:00
abstract::The 32 kDa hydrophilic and acidic enamelin, the most stable cleavage fragment of the enamel specific glycoprotein, is believed to play vital roles in controlling crystal nucleation or growth during enamel biomineralization. Circular dichroism and Fourier transform infrared spectra demonstrate that the secondary struct...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2008.04.007
更新日期:2008-07-01 00:00:00
abstract::We have used conical tomography to study the structure of integral proteins in their phospholipid bilayer environments. Complete conical series were collected from replicas of the water channel aquaporin-0 (AQP0), a 6.6 nm side tetramer with a molecular weight of approximately 120 kDa that was purified and reconstitut...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2004.09.004
更新日期:2005-01-01 00:00:00
abstract::The optimal balance of cellular nucleotides and the efficient elimination of non-canonical nucleotides are critical to avoiding erroneous mutation during DNA replication. One such mechanism involves the degradation of excessive or abnormal nucleotides by nucleotide-hydrolyzing enzymes. YpgQ contains the histidine-aspa...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.04.002
更新日期:2016-07-01 00:00:00
abstract::We have shown by in vitro development of staged follicles in the presence of tritiated proline, as well as by immunoblot analysis, that the Dvs19 and DVS15 chorion proteins of Drosophila virilis are synthesized by the follicular epithelium and are incorporated in the chorion at the terminal stages of choriogenesis. Li...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1998.4999
更新日期:1998-10-01 00:00:00
abstract::The Bsoft package is aimed at processing electron micrographs for the determination of the three-dimensional structures of biological specimens. Recent advances in hardware allow us to solve structures to near atomic resolution using single particle analysis (SPA). The Map Challenge offered me an opportunity to test t...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.07.003
更新日期:2018-10-01 00:00:00
abstract::A new scanning probe microscope, the photonic force microscope (PFM), based on optical tweezers and two-photon absorption processes for biological applications is described. Optical tweezers are used to trap a fluorescent latex bead with a diameter of 200 nm in an aqueous solution in all three dimensions. The fluoresc...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1997.3880
更新日期:1997-07-01 00:00:00
abstract::A novel preparation of spontaneously contracting heart cells embedded in a collagen strand provides an ideal experimental system for correlative structure-function experiments that utilize the techniques of electron microscopy, quantitative electron probe x-ray microanalysis (EPXMA) and imaging. Heart cells grown with...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(91)90061-z
更新日期:1991-02-01 00:00:00
abstract::Uptake and metabolism of silicon by diatoms are studied by the combined use of solid-state 29Si NMR spectroscopy and confocal laser fluorescence microscopy especially with respect to the presence and nature of an intracellular silicon-storage pool. Cells of the marine diatom Thalassiosira pseudonana were synchronized ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.09.010
更新日期:2008-01-01 00:00:00
abstract::Vateritic deformities occurring in the invasive heterodont bivalve Corbicula fluminea from several locations in the UK were characterised in detail for the first time using scanning electron microscopy, X-ray diffraction and different geochemical techniques (electron microprobe, ICP-AES, and mass spectrometry). Large ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.02.002
更新日期:2011-05-01 00:00:00
abstract::Chorismate pathway enzymes are important as producers of nonnucleotide aromatic compounds. The enzyme chorismate lyase from Escherichia coli has been crystallized in four distinct forms, three of which have been characterized by X-ray diffraction. Despite widespread screening, all four crystal forms grow from the same...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1999.4205
更新日期:2000-02-01 00:00:00
abstract::We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all imag...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2017.09.007
更新日期:2017-11-01 00:00:00
abstract::REMORINs are nanodomain-organized proteins located in the plasma membrane and involved in cellular responses in plants. The dynamic assembly of the membrane nanodomains represents an essential tool of the versatile membrane barriers to control and modulate cellular functions. Nevertheless, the assembly mechanisms and ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.02.003
更新日期:2019-04-01 00:00:00
abstract::Biophysical cues such as substrate modulus have been shown to influence a variety of cell behaviors. We have determined the elastic modulus of the anterior basement membrane and Descemet's membrane of the human cornea with atomic force microscopy (AFM). A spherical probe was used with a radius approximating that of a ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2009.03.012
更新日期:2009-07-01 00:00:00
abstract::Charge contrast imaging (CCI) is a dynamic phenomenon recently reported in insulating and semiconducting materials imaged with low vacuum or variable pressure scanning electron microscopes (SEM). Data presented in this paper illustrates that CCI can also be applied to biominerals and biological soft-tissues and that u...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.04.004
更新日期:2006-09-01 00:00:00
abstract::Different types of cells have been imaged with the atomic force microscope. The morphology of the archaebacterium Halobacterium halobium in its dry state was revealed. On a leaf of the small Indian tree Lagerstroemia subcostata a stoma was imaged. The lower side of a water lily leaf was imaged in water showing feature...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(90)90098-w
更新日期:1990-10-01 00:00:00
abstract::Nacre has long served as a model for understanding the biomineralization mechanism and designing bio-inspired materials. However, its basic building blocks, the aragonite tablets, are still under debate in terms of their fine structure at the nanoscale and corresponding formation mechanism. Here, using a field emissio...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.01.010
更新日期:2013-04-01 00:00:00
abstract::The structure of full-length human TLR5 determined by electron microscopy single-particle image reconstruction at 26Å resolution shows that TLR5 forms an asymmetric homodimer via ectodomain interactions. The structure shows that like TLR9, TLR5 dimerizes in the absence of ligand. The asymmetry of the dimer suggests th...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.12.002
更新日期:2012-02-01 00:00:00
abstract::The morphologic effects of different sulfur-substituted mono- and dicarboxylic fatty acids on rat hepatocytes have been examined. The substance 1,10-biscarboxymethylthiodecane (BCMTD) is blocked for both beta- and omega-oxidation, whereas 1-monocarboxymethylthiodecane (CMTTD) is only non-beta-oxidizable. At equimolar ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/1047-8477(90)90044-d
更新日期:1990-05-01 00:00:00
abstract::Long-depth imaging of specific gene expression in the midgestation whole-mount mouse embryo (WME) is demonstrated with single-photon excitation (1PE) confocal fluorescence microscopy and fluorescence in situ hybridization. Expression domains of Pax-6 mRNA transcripts were labeled with an in situ hybridization probe th...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2000.4238
更新日期:2000-07-01 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::The repetitive Gly-X-Y sequence is the telltale sign of triple helical domains in collagens and collagen-like proteins. Most collagen sequences contain sporadic interruptions of this pattern, which may have functional roles in molecular flexibility, assembly or molecular recognition. However, the structural signatures...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2014.03.022
更新日期:2014-06-01 00:00:00
abstract::The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles,...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.10.012
更新日期:2013-01-01 00:00:00
abstract::TheL-A virus (LAV) particle is a specialized compartment for the transcription and replication of double-stranded RNA. It is 390 A in diameter and infects yeast. The particle is formed by a capsid containing 120 copies of a 680-residue gene product arranged with T = 1 icosahedral symmetry, approximately two copies of ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2001.4371
更新日期:2001-07-01 00:00:00
abstract::The biomechanical properties of the zone of calcified cartilage (ZCC) in articulating joints are of clinical relevance due to the role ZCC plays in load transfer from cartilage to bone. To determine the micron-level mechanical properties and their correlation to mineral concentration in the ZCC, we combined nanoindent...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2004.10.010
更新日期:2005-02-01 00:00:00
abstract::In cryo-electron microscopy (cryo-EM) single-particle reconstruction, the heterogeneity of two-dimensional projection image data resulting from the co-existence of different conformational or ligand binding states of a macromolecular complex remains a major obstacle as it impairs the validity of reconstructed density ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.06.012
更新日期:2007-01-01 00:00:00
abstract::Tricorn protease from Thermoplasma acidophilum is a hexameric enzyme; in vivo the hexamers assemble further to form large icosahedral capsids of 14.6 MDa. Recombinant Tricorn protease was purified as an enzymatically active hexamer of 0.72 MDa that formed crystals of octahedral morphology under low-ionic-strength cond...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.2001.4360
更新日期:2001-04-01 00:00:00