scholarly journals Crystal structures and functional analysis of the ZnF5-WWE1-WWE2 region of PARP13/ZAP define a new mode of engaging poly(ADP-ribose)

2021 ◽  
Author(s):  
Jijin R.A. Kuttiyatveetil ◽  
Heddy Soufari ◽  
Morgan Dasovich ◽  
Isabel R. Uribe ◽  
Shang-Jung Cheng ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Pocket ◽  
Polymer Chains ◽  
Binding Studies ◽  
Rna Detection ◽  
Structural Framework ◽  
Preferential Binding ◽  
Extended Surface ◽  
And Function ◽  
Adp Ribosyltransferase

PARP13/ZAP acts against multiple viruses through recognizing and promoting degradation of cytoplasmic viral mRNA. PARP13 has four N-terminal Zn-finger motifs that bind CG-rich nucleotide sequences, and a C-terminal ADP ribosyltransferase fold similar to other PARPs. A central region predicted to contain a fifth Zn-finger and two tandem WWE domains is implicated in binding poly(ADP-ribose); however, there are limited insights into the structure and function of this PARP13 region (ZnF5-WWE1-WWE2). Here, we present crystal structures of ZnF5-WWE1-WWE2 from mouse PARP13 in complex with ADP-ribose and with ATP. ZnF5-WWE1-WWE2 crystallized as a dimer with major contacts formed between WWE1 and WWE2 originating from different monomers, indicative of a more compact monomeric arrangement of the tandem WWE domains. Solution scattering experiments and biophysical analysis indicated a monomer in solution, suggesting that the crystal dimer represents domain swapping that could potentially represent a PARP13 conformation assumed when signaling viral RNA detection. The crystal structure and binding studies demonstrate that WWE2 interacts with ADP-ribose and ATP, whereas WWE1 does not have a functional binding site. The shape of the WWE2 binding pocket disfavors interaction with the ribose-ribose linkage of poly(ADP-ribose). Binding studies with poly(ADP-ribose) ligands indicate that WWE2 serves as an anchor for preferential binding to the terminal end of poly(ADP-ribose), and the composite structure of ZnF5-WWE1-WWE2 forms an extended surface to engage polymer chains of ADP-ribose. This model represents a novel mode of poly(ADP-ribose) recognition and provides a structural framework for investigating poly(ADP-ribose) impact on PARP13 function.

scholarly journals The Crystal Structures of Chikungunya and Venezuelan Equine Encephalitis Virus nsP3 Macro Domains Define a Conserved Adenosine Binding Pocket

2009 ◽  
Vol 83 (13) ◽  
pp. 6534-6545 ◽  
Author(s):  
Hélène Malet ◽  
Bruno Coutard ◽  
Saïd Jamal ◽  
Hélène Dutartre ◽  
Nicolas Papageorgiou ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Chikungunya Virus ◽  
Binding Pocket ◽  
Venezuelan Equine Encephalitis Virus ◽  
Encephalitis Virus ◽  
Venezuelan Equine Encephalitis ◽  
Binding Studies ◽  
Equine Encephalitis Virus ◽  
Macro Domain

ABSTRACT Macro domains (also called “X domains”) constitute a protein module family present in all kingdoms of life, including viruses of the Coronaviridae and Togaviridae families. Crystal structures of the macro domain from the Chikungunya virus (an “Old World” alphavirus) and the Venezuelan equine encephalitis virus (a “New World” alphavirus) were determined at resolutions of 1.65 and 2.30 Å, respectively. These domains are active as adenosine di-phosphoribose 1″-phosphate phosphatases. Both the Chikungunya and the Venezuelan equine encephalitis virus macro domains are ADP-ribose binding modules, as revealed by structural and functional analysis. A single aspartic acid conserved through all macro domains is responsible for the specific binding of the adenine base. Sequence-unspecific binding to long, negatively charged polymers such as poly(ADP-ribose), DNA, and RNA is observed and attributed to positively charged patches outside of the active site pocket, as judged by mutagenesis and binding studies. The crystal structure of the Chikungunya virus macro domain with an RNA trimer shows a binding mode utilizing the same adenine-binding pocket as ADP-ribose, but avoiding the ADP-ribose 1″-phosphate phosphatase active site. This leaves the AMP binding site as the sole common feature in all macro domains.

Crystal Structures of Fragments D and Double-D from Fibrinogen and Fibrin

1999 ◽  
Vol 82 (08) ◽  
pp. 271-276 ◽  
Author(s):  
Glen Spraggon ◽  
Stephen Everse ◽  
Russell Doolittle
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Crystal Structures ◽  
Structure And Function ◽  
X Ray ◽  
Long Period ◽  
And Function

IntroductionAfter a long period of anticipation,1 the last two years have witnessed the first high-resolution x-ray structures of fragments from fibrinogen and fibrin.2-7 The results confirmed many aspects of fibrinogen structure and function that had previously been inferred from electron microscopy and biochemistry and revealed some unexpected features. Several matters have remained stubbornly unsettled, however, and much more work remains to be done. Here, we review several of the most significant findings that have accompanied the new x-ray structures and discuss some of the problems of the fibrinogen-fibrin conversion that remain unresolved. * Abbreviations: GPR—Gly-Pro-Arg-derivatives; GPRPam—Gly-Pro-Arg-Pro-amide; GHRPam—Gly-His-Arg-Pro-amide

scholarly journals Manipulating the Conformation of 3,2′:6′,3″-Terpyridine in [Cu2(μ-OAc)4(3,2′:6′,3″-tpy)]n 1D-Polymers

Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 182-198
Author(s):  
Dalila Rocco ◽  
Samantha Novak ◽  
Alessandro Prescimone ◽  
Edwin C. Constable ◽  
Catherine E. Housecroft
Keyword(s):  
Single Crystal ◽  
Crystal Structures ◽  
Metal Binding ◽  
Polymer Chains ◽  
X Ray Diffraction ◽  
Face To Face ◽  
Single Crystal Structures ◽  
Π Stacking ◽  
Metal Binding Domain ◽  
Packing Interactions

We report the preparation and characterization of 4′-([1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (1), 4′-(4′-fluoro-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (2), 4′-(4′-chloro-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (3), 4′-(4′-bromo-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (4), and 4′-(4′-methyl-[1,1′-biphenyl]-4-yl)-3,2′:6′,3″-terpyridine (5), and their reactions with copper(II) acetate. Single-crystal structures of the [Cu2(μ-OAc)4L]n 1D-coordination polymers with L = 1–5 have been determined, and powder X-ray diffraction confirms that the single crystal structures are representative of the bulk samples. [Cu2(μ-OAc)4(1)]n and [Cu2(μ-OAc)4(2)]n are isostructural, and zigzag polymer chains are present which engage in π-stacking interactions between [1,1′-biphenyl]pyridine units. 1D-chains nest into one another to give 2D-sheets; replacing the peripheral H in 1 by an F substituent in 2 has no effect on the solid-state structure, indicating that bifurcated contacts (H...H for 1 or H...F for 2) are only secondary packing interactions. Upon going from [Cu2(μ-OAc)4(1)]n and [Cu2(μ-OAc)4(2)]n to [Cu2(μ-OAc)4(3)]n, [Cu2(μ-OAc)4(4)]n, and [Cu2(μ-OAc)4(5)]n·nMeOH, the increased steric demands of the Cl, Br, or Me substituent induces a switch in the conformation of the 3,2′:6′,3″-tpy metal-binding domain, and a concomitant change in dominant packing interactions to py–py and py–biphenyl face-to-face π-stacking. The study underlines how the 3,2′:6′,3″-tpy domain can adapt to different steric demands of substituents through its conformational flexibility.

scholarly journals Structural basis of adhesive binding by desmocollins and desmogleins

2016 ◽  
Vol 113 (26) ◽  
pp. 7160-7165 ◽  
Author(s):  
Oliver J. Harrison ◽  
Julia Brasch ◽  
Gorka Lasso ◽  
Phinikoula S. Katsamba ◽  
Goran Ahlsen ◽  
...  
Keyword(s):  
Amino Acids ◽  
Crystal Structures ◽  
Structural Basis ◽  
Cellular Interactions ◽  
Opposite Charge ◽  
Charged Amino Acids ◽  
Structural Framework ◽  
Classical Cadherins ◽  
Coated Bead

Desmosomes are intercellular adhesive junctions that impart strength to vertebrate tissues. Their dense, ordered intercellular attachments are formed by desmogleins (Dsgs) and desmocollins (Dscs), but the nature of trans-cellular interactions between these specialized cadherins is unclear. Here, using solution biophysics and coated-bead aggregation experiments, we demonstrate family-wise heterophilic specificity: All Dsgs form adhesive dimers with all Dscs, with affinities characteristic of each Dsg:Dsc pair. Crystal structures of ectodomains from Dsg2 and Dsg3 and from Dsc1 and Dsc2 show binding through a strand-swap mechanism similar to that of homophilic classical cadherins. However, conserved charged amino acids inhibit Dsg:Dsg and Dsc:Dsc interactions by same-charge repulsion and promote heterophilic Dsg:Dsc interactions through opposite-charge attraction. These findings show that Dsg:Dsc heterodimers represent the fundamental adhesive unit of desmosomes and provide a structural framework for understanding desmosome assembly.

scholarly journals Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

2017 ◽  
Vol 73 (4) ◽  
pp. 294-315 ◽  
Author(s):  
Kimberly A. Stanek ◽  
Jennifer Patterson-West ◽  
Peter S. Randolph ◽  
Cameron Mura
Keyword(s):  
Rna Binding ◽  
Binding Pocket ◽  
Binding Mode ◽  
Evolutionary Conservation ◽  
Aquifex Aeolicus ◽  
Binding Properties ◽  
Bacterial Phyla ◽  
Mrna Targets ◽  
Small Regulatory Rnas ◽  
And Function

The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophileAquifex aeolicus(Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore,AaeHfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures ofAaeHfq were determined in space groupsP1 andP6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6RNA reveals that the outer rim of theAaeHfq hexamer features a well defined binding pocket that is selective for uracil. ThisAaeHfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

Syntheses, crystal structures and DNA-binding studies of Cu(II) and Zn(II) complexes bearing asymmetrical aroylhydrazone ligand

2017 ◽  
Vol 1130 ◽  
pp. 818-828 ◽  
Author(s):  
Yueqin Li ◽  
Zhiwei Yang ◽  
Minya Zhou ◽  
Jing He ◽  
Xuehong Wang ◽  
...  
Keyword(s):  
Dna Binding ◽  
Crystal Structures ◽  
Binding Studies ◽  
Dna Binding Studies

scholarly journals Structure and function of cytochromes P450:a comparative analysis of three crystal structures

Structure ◽  
1995 ◽  
Vol 3 (1) ◽  
pp. 41-62 ◽  
Author(s):  
Charles A Hasemann ◽  
Ravi G Kurumbail ◽  
Sekhar S Boddupalli ◽  
Julian A Peterson ◽  
Johann Deisenhofer
Keyword(s):  
Comparative Analysis ◽  
Crystal Structures ◽  
Cytochromes P450 ◽  
Structure And Function ◽  
And Function

scholarly journals Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2

2009 ◽  
Vol 106 (37) ◽  
pp. 15616-15621 ◽  
Author(s):  
Masataka Umitsu ◽  
Hiroshi Nishimasu ◽  
Akiko Noma ◽  
Tsutomu Suzuki ◽  
Ryuichiro Ishitani ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Pocket ◽  
Structural Basis ◽  
Binding Modes ◽  
Substrate Binding Pocket ◽  
Methyl Group ◽  
Group Transfer ◽  
Canonical Class ◽  
Functional Analyses

S-adenosylmethionine (AdoMet) is a methyl donor used by a wide variety of methyltransferases, and it is also used as the source of an α-amino-α-carboxypropyl (“acp”) group by several enzymes. tRNA-yW synthesizing enzyme-2 (TYW2) is involved in the biogenesis of a hypermodified nucleotide, wybutosine (yW), and it catalyzes the transfer of the “acp” group from AdoMet to the C7 position of the imG-14 base, a yW precursor. This modified nucleoside yW is exclusively located at position 37 of eukaryotic tRNAPhe, and it ensures the anticodon-codon pairing on the ribosomal decoding site. Although this “acp” group has a significant role in preventing decoding frame shifts, the mechanism of the “acp” group transfer by TYW2 remains unresolved. Here we report the crystal structures and functional analyses of two archaeal homologs of TYW2 from Pyrococcus horikoshii and Methanococcus jannaschii. The in vitro mass spectrometric and radioisotope-labeling analyses confirmed that these archaeal TYW2 homologues have the same activity as yeast TYW2. The crystal structures verified that the archaeal TYW2 contains a canonical class-I methyltransferase (MTase) fold. However, their AdoMet-bound structures revealed distinctive AdoMet-binding modes, in which the “acp” group, instead of the methyl group, of AdoMet is directed to the substrate binding pocket. Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the “acp” group, and not the methyl group, from AdoMet to the nucleobase.

scholarly journals In-silico prediction and observations of nuclear matrix attachment

2006 ◽  
Vol 11 (2) ◽  
Author(s):  
Adrian Platts ◽  
Amelia Quayle ◽  
Stephen Krawetz
Keyword(s):  
Nuclear Matrix ◽  
In Silico ◽  
Sequence Similarity ◽  
Loop Model ◽  
Simple Loop ◽  
Structural Framework ◽  
The Subject ◽  
In Silico Predictions ◽  
The One ◽  
And Function

AbstractThe nuclear matrix is a functionally adaptive structural framework interior to the nuclear envelope. The nature and function of this nuclear organizer remains the subject of widespread discussion in the epigenetic literature. To draw this discussion together with a view to suggest a way forward we summarize the biochemical evidence for the modalities of DNA-matrix binding alongside the in-silico predictions. Concordance is exhibited at various, but not all levels. On the one hand, both the reiteration and sequence similarity of some elements of Matrix Attachment Regions suggest conservation. On the other hand, in-silico predictions suggest additional unique components. In bringing together biological and sequence evidence we conclude that binding may be hierarchical in nature, reflective of a biological role in replicating, transcribing and potentiating chromatin. Nuclear matrix binding may well be more complex than the widely accepted simple loop model.

Abstract 380: SAA Lipidation and Delipidation by Hepatocytes

2017 ◽  
Vol 37 (suppl_1) ◽  
Author(s):  
Ailing Ji ◽  
Akinwunmi Akinmusire ◽  
Maria C de Beer ◽  
Frederick C de Beer ◽  
Nancy R Webb ◽  
...  
Keyword(s):  
Acute Phase ◽  
Serum Amyloid A ◽  
Free Form ◽  
Primary Hepatocytes ◽  
Binding Studies ◽  
Acute Phase Reactants ◽  
Amyloid A ◽  
Large Particles ◽  
And Function ◽  
Deficient Mice

Serum amyloid A (SAA) is one of the most striking acute phase reactants that can rapidly increase 1000-fold in plasma concentration in response to inflammatory cytokines. SAA in lipid-free form exhibits pro-inflammatory activities, but its putative physiological function(s) are poorly understood. SAA is produced and secreted largely by the liver and is present in plasma mainly as an HDL apolipoprotein. The pathways by which SAA is lipidated and incorporated into HDL are poorly understood. Plasma SAA is cleared more rapidly than the other major HDL apolipoproteins, but pathways involved in its delipidation and plasma clearance have also not been defined. In this study we examined how SAA is lipidated in primary hepatocytes and how such lipidation relates to the formation of nascent HDL particles. Endogenous hepatocyte SAA was lipidated and released from cells as large particles that were distinct from apoA-I-containing nascent HDL’s. Unlike apoA-I, formation of these SAA-containing particles was independent of ABCA-I. Similarly, when SAA was exogenously added to cells, SAA was lipidated to form nascent particles that were distinct from apoA-I-containing particles. We further studied the interaction of lipid-free and HDL-bound SAA with hepatocytes. Both in lipid-free form and as part of HDL, SAA exhibited significantly greater binding to cells than apoA-I or apoA-II. Binding studies were also carried out with normal and acute phase HDL’s isolated from control and SAA-deficient mice. Together, the results suggested that SAA, unlike apoA-I, is selectively removed from HDL by binding to hepatocytes. These findings may provide new insights into SAA metabolism and function.

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