scholarly journals Domain Architecture in Homolog Identification

2006 ◽  
pp. 11-23
Author(s):  
N. Song ◽  
R. D. Sedgewick ◽  
D. Durand
Keyword(s):  
Domain Architecture

Plant carotenoid cleavage oxygenases: structure–function relationships and role in development and metabolism

2019 ◽  
Vol 19 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Manoj Kumar Dhar ◽  
Sonal Mishra ◽  
Archana Bhat ◽  
Sudha Chib ◽  
Sanjana Kaul
Keyword(s):  
Higher Plants ◽  
Domain Architecture ◽  
Heme Iron ◽  
Critical Assessment ◽  
Protein Family ◽  
Regulatory Mechanisms ◽  
Non Heme Iron ◽  
Functional Aspects ◽  
Functional Understanding ◽  
Signal Production

Abstract A plant communicates within itself and with the outside world by deploying an array of agents that include several attractants by virtue of their color and smell. In this category, the contribution of ‘carotenoids and apocarotenoids’ is very significant. Apocarotenoids, the carotenoid-derived compounds, show wide representation among organisms. Their biosynthesis occurs by oxidative cleavage of carotenoids, a high-value reaction, mediated by carotenoid cleavage oxygenases or carotenoid cleavage dioxygenases (CCDs)—a family of non-heme iron enzymes. Structurally, this protein family displays wide diversity but is limited in its distribution among plants. Functionally, this protein family has been recognized to offer a role in phytohormones, volatiles and signal production. Further, their wide presence and clade-specific functional disparity demands a comprehensive account. This review focuses on the critical assessment of CCDs of higher plants, describing recent progress in their functional aspects and regulatory mechanisms, domain architecture, classification and localization. The work also highlights the relevant discussion for further exploration of this multi-prospective protein family for the betterment of its functional understanding and improvement of crops.

scholarly journals Crystal Structure ofDeinococcus radioduransRecQ Helicase Catalytic Core Domain: The Interdomain Flexibility

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Sheng-Chia Chen ◽  
Chi-Hung Huang ◽  
Chia Shin Yang ◽  
Tzong-Der Way ◽  
Ming-Chung Chang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Deinococcus Radiodurans ◽  
Domain Architecture ◽  
Genome Integrity ◽  
Catalytic Core Domain ◽  
Catalytic Core ◽  
Core Domain ◽  
Winged Helix ◽  
Dna Helicases ◽  
E Coli

RecQ DNA helicases are key enzymes in the maintenance of genome integrity, and they have functions in DNA replication, recombination, and repair. In contrast to most RecQs, RecQ fromDeinococcus radiodurans(DrRecQ) possesses an unusual domain architecture that is crucial for its remarkable ability to repair DNA. Here, we determined the crystal structures of the DrRecQ helicase catalytic core and its ADP-bound form, revealing interdomain flexibility in its first RecA-like and winged-helix (WH) domains. Additionally, the WH domain of DrRecQ is positioned in a different orientation from that of theE. coliRecQ (EcRecQ). These results suggest that the orientation of the protein during DNA-binding is significantly different when comparing DrRecQ and EcRecQ.

scholarly journals Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein

Virology ◽  
2008 ◽  
Vol 378 (2) ◽  
pp. 282-291 ◽  
Author(s):  
Ping Yuan ◽  
George P. Leser ◽  
Borries Demeler ◽  
Robert A. Lamb ◽  
Theodore S. Jardetzky
Keyword(s):  
Domain Architecture

scholarly journals 3P268 A domain architecture analysis in single-spanning transmembrane proteins

2004 ◽  
Vol 44 (supplement) ◽  
pp. S256
Author(s):  
M. Arai ◽  
T. Fukushi ◽  
S. Mizuta ◽  
M. Satake ◽  
T. Shimizu
Keyword(s):  
Domain Architecture ◽  
Transmembrane Proteins ◽  
Architecture Analysis

scholarly journals The Crystal Structure of the Rare-Cutting Restriction Enzyme SdaI Reveals Unexpected Domain Architecture

Structure ◽  
2006 ◽  
Vol 14 (9) ◽  
pp. 1389-1400 ◽  
Author(s):  
Giedre Tamulaitiene ◽  
Arturas Jakubauskas ◽  
Claus Urbanke ◽  
Robert Huber ◽  
Saulius Grazulis ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Restriction Enzyme ◽  
Domain Architecture

scholarly journals The malaria circumsporozoite protein has two functional domains, each with distinct roles as sporozoites journey from mosquito to mammalian host

2011 ◽  
Vol 208 (2) ◽  
pp. 341-356 ◽  
Author(s):  
Alida Coppi ◽  
Ramya Natarajan ◽  
Gabriele Pradel ◽  
Brandy L. Bennett ◽  
Eric R. James ◽  
...  
Keyword(s):  
Vaccine Development ◽  
Critical Role ◽  
Domain Architecture ◽  
Surface Protein ◽  
Circumsporozoite Protein ◽  
Mammalian Host ◽  
Multifunctional Protein ◽  
Mosquito Midgut ◽  
Cell Adhesive ◽  
Mammalian Liver

Plasmodium sporozoites make a remarkable journey from the mosquito midgut to the mammalian liver. The sporozoite’s major surface protein, circumsporozoite protein (CSP), is a multifunctional protein required for sporozoite development and likely mediates several steps of this journey. In this study, we show that CSP has two conformational states, an adhesive conformation in which the C-terminal cell-adhesive domain is exposed and a nonadhesive conformation in which the N terminus masks this domain. We demonstrate that the cell-adhesive domain functions in sporozoite development and hepatocyte invasion. Between these two events, the sporozoite must travel from the mosquito midgut to the mammalian liver, and N-terminal masking of the cell-adhesive domain maintains the sporozoite in a migratory state. In the mammalian host, proteolytic cleavage of CSP regulates the switch to an adhesive conformation, and the highly conserved region I plays a critical role in this process. If the CSP domain architecture is altered such that the cell-adhesive domain is constitutively exposed, the majority of sporozoites do not reach their target organs, and in the mammalian host, they initiate a blood stage infection directly from the inoculation site. These data provide structure–function information relevant to malaria vaccine development.

scholarly journals Cell Cycle Localization, Dimerization, and Binding Domain Architecture of the Telomere Protein cPot1

2004 ◽  
Vol 24 (5) ◽  
pp. 2091-2102 ◽  
Author(s):  
Chao Wei ◽  
Carolyn M. Price
Keyword(s):  
Cell Cycle ◽  
Dna Binding ◽  
Binding Site ◽  
Domain Architecture ◽  
Binding Domain ◽  
Binding Motif ◽  
Dna Binding Domain ◽  
Telomere Protein ◽  
Ob Fold

ABSTRACT Pot1 is a single-stranded-DNA-binding protein that recognizes telomeric G-strand DNA. It is essential for telomere capping in Saccharomyces pombe and regulates telomere length in humans. Human Pot1 also interacts with proteins that bind the duplex region of the telomeric tract. Thus, like Cdc13 from S. cerevisiae, Pot 1 may have multiple roles at the telomere. We show here that endogenous chicken Pot1 (cPot1) is present at telomeres during periods of the cell cycle when t loops are thought to be present. Since cPot1 can bind internal loops and directly adjacent DNA-binding sites, it is likely to fully coat and protect both G-strand overhangs and the displaced G strand of a t loop. The minimum binding site of cPot1 is double that of the S. pombe DNA-binding domain. Although cPot can self associate, dimerization is not required for DNA binding and hence does not explain the binding-site duplication. Instead, the DNA-binding domain appears to be extended to contain a second binding motif in addition to the conserved oligonucleotide-oligosaccharide (OB) fold present in other G-strand-binding proteins. This second motif could be another OB fold. Although dimerization is inefficient in vitro, it may be regulated in vivo and could promote association with other telomere proteins and/or telomere compaction.

scholarly journals Proteomic and biochemical comparison of the cellular interaction partners of human VPS33A and VPS33B

2017 ◽  
Author(s):  
Morag R. Hunter ◽  
Geoffrey G. Hesketh ◽  
Anne-Claude Gingras ◽  
Stephen C. Graham
Keyword(s):  
Sequence Similarity ◽  
Domain Architecture ◽  
Gel Filtration ◽  
Cellular Interaction ◽  
Class Iii ◽  
Phosphatidylinositol 3 Kinase ◽  
Protein Subunit ◽  
Over Expression ◽  
Biochemical Comparison

ABSTRACTMulti-subunit tethering complexes control membrane fusion events in eukaryotic cells. CORVET and HOPS are two such multi-subunit tethering complexes, both containing the Sec1/Munc18 protein subunit VPS33A. Metazoans additionally possess VPS33B, which has considerable sequence similarity to VPS33A but does not integrate into CORVET or HOPS complexes and instead stably interacts with VIPAR. It has been recently suggested that VPS33B and VIPAR comprise two subunits of a novel multi-subunit tethering complex (named ‘CHEVI’), analogous in configuration to CORVET and HOPS. We utilised the BioID proximity biotinylation assay to compare and contrast the interactomes of VPS33A and VPS33B. Overall, few proteins were identified as associating with both VPS33A and VPS33B, suggesting these proteins have distinct sub-cellular localisations. Consistent with previous reports, we observed that VPS33A was co-localised with many components of class III phosphatidylinositol 3-kinase (PI3KC3) complexes: PIK3C3, PIK3R4, NRBF2, UVRAG and RUBICON. Although in this assay VPS33A clearly co-localised with several subunits of CORVET and HOPS, no proteins with the canonical CORVET/HOPS domain architecture were found to co-localise with VPS33B. Instead, we identified two novel VPS33B-interacting proteins, VPS53 and CCDC22. CCDC22 co-immunoprecipitated with VPS33B and VIPAR in over-expression conditions and interacts directly with the VPS33B-VIPAR complex in vitro. However, CCDC22 does not appear to co-fractionate with VPS33B and VIPAR in gel filtration of human cell lysates. We also observed that the protein complex in HEK293T cells which contained VPS33B and VIPAR was considerably smaller than CORVET/HOPS, suggesting that, unlike VPS33A, VPS33B does not assemble into a large stable multi-subunit tethering complex.

scholarly journals Molecular Basis of Antibiotic Self-Resistance in a Bee Larvae Pathogen

2021 ◽  
Author(s):  
Tam Dang ◽  
Bernhard Loll ◽  
Sebastian Müller ◽  
Ranko Skobalj ◽  
Julia Ebeling ◽  
...  
Keyword(s):  
Domain Architecture ◽  
Biosynthetic Gene Cluster ◽  
American Foulbrood ◽  
Antibacterial And Antifungal Activity ◽  
Gene Coding ◽  
Acetylation Site ◽  
Terminal Amino ◽  
Binding Groove ◽  
Bee Disease ◽  
Antibacterial And Antifungal

Paenibacillus larvae, the causative agent of the devastating honey-bee disease American Foulbrood, produces the cationic polyketide-peptide hybrid paenilamicin that displays high antibacterial and antifungal activity. Its biosynthetic gene cluster contains a gene coding for the N-acetyltransferase PamZ. We show that PamZ acts as self-resistance factor in P. larvae by deactivation of paenilamicin. Using tandem MS, NMR spectroscopy and synthetic diastereomers, we identified the N-terminal amino group of the agmatinamic acid as the N-acetylation site. These findings highlight the pharmacophore region of paenilamicin, which we very recently identified as a new ribosome inhibitor. Here, we further elucidated the crystal structure of PamZ:acetyl-CoA complex at 1.34 Å resolution. An unusual tandem-domain architecture provides a well-defined substrate-binding groove decorated with negatively-charged residues to specifically attract the cationic paenilamicin. Our results will help to understand the mode of action of paenilamicin and its role in pathogenicity of P. larvae to fight American Foulbrood.

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