Protein Architecture

Hematology ◽  
2018 ◽  
pp. 59-67
Author(s):  
Jia-huai Wang ◽  
Michael J. Eck
Keyword(s):  
Protein Architecture

scholarly journals A high-resolution protein architecture of the budding yeast genome

Nature ◽  
2021 ◽  
Author(s):  
Matthew J. Rossi ◽  
Prashant K. Kuntala ◽  
William K. M. Lai ◽  
Naomi Yamada ◽  
Nitika Badjatia ◽  
...  
Keyword(s):  
High Resolution ◽  
Budding Yeast ◽  
Yeast Genome ◽  
Protein Architecture

scholarly journals Evolutionary Analysis of Cystatins of Early-Emerging Metazoans Reveals a Novel Subtype in Parasitic Cnidarians

Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 110
Author(s):  
Pavla Bartošová-Sojková ◽  
Jiří Kyslík ◽  
Gema Alama-Bermejo ◽  
Ashlie Hartigan ◽  
Stephen D. Atkinson ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Organization ◽  
Gene Repertoire ◽  
Evolutionary Analysis ◽  
Ancestral Gene ◽  
Protein Architecture ◽  
Basal Metazoan ◽  
Cystatin Gene ◽  
Evolutionary Aspects

The evolutionary aspects of cystatins are greatly underexplored in early-emerging metazoans. Thus, we surveyed the gene organization, protein architecture, and phylogeny of cystatin homologues mined from 110 genomes and the transcriptomes of 58 basal metazoan species, encompassing free-living and parasite taxa of Porifera, Placozoa, Cnidaria (including Myxozoa), and Ctenophora. We found that the cystatin gene repertoire significantly differs among phyla, with stefins present in most of the investigated lineages but with type 2 cystatins missing in several basal metazoan groups. Similar to liver and intestinal flukes, myxozoan parasites possess atypical stefins with chimeric structure that combine motifs of classical stefins and type 2 cystatins. Other early metazoan taxa regardless of lifestyle have only the classical representation of cystatins and lack multi-domain ones. Our comprehensive phylogenetic analyses revealed that stefins and type 2 cystatins clustered into taxonomically defined clades with multiple independent paralogous groups, which probably arose due to gene duplications. The stefin clade split between the subclades of classical stefins and the atypical stefins of myxozoans and flukes. Atypical stefins represent key evolutionary innovations of the two parasite groups for which their origin might have been linked with ancestral gene chimerization, obligate parasitism, life cycle complexity, genome reduction, and host immunity.

scholarly journals Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Karthik Ramanadane ◽  
Monique S Straub ◽  
Raimund Dutzler ◽  
Cristina Manatschal
Keyword(s):  
Hydration Shell ◽  
Transition Metal Ions ◽  
Ion Binding ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein Architecture ◽  
Large Pool ◽  
Structural And Functional Properties ◽  
The Family ◽  
Magnesium Transporter

Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca2+ and Mg2+, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H+ serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg2+. The protein transports Mg2+ and Mn2+ but not Ca2+ by a mechanism that is not coupled to H+. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.

scholarly journals Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex

2021 ◽  
Vol 118 (48) ◽  
pp. e2112107118
Author(s):  
Eduardo M. Bruch ◽  
Pierre Vilela ◽  
Lu Yang ◽  
Alexandra Boyko ◽  
Norik Lexa-Sapart ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Metabolic Engineering ◽  
High Molecular Weight ◽  
Protein Oligomerization ◽  
Central Metabolism ◽  
Hollow Core ◽  
Protein Architecture ◽  
Unique Protein ◽  
Gene Coding

α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high–molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an odhA gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.

scholarly journals LRRpredictor—A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 286 ◽  
Author(s):  
Eliza C. Martin ◽  
Octavina C. A. Sukarta ◽  
Laurentiu Spiridon ◽  
Laurentiu G. Grigore ◽  
Vlad Constantinescu ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Structural Data ◽  
Innate Immune ◽  
Protein Protein Interactions ◽  
Ensemble Of Classifiers ◽  
Immune Receptor ◽  
Motif Detection ◽  
Protein Architecture ◽  
Recognition Specificity ◽  
Leucine Rich Repeats

Leucine-rich-repeats (LRRs) belong to an archaic procaryal protein architecture that is widely involved in protein–protein interactions. In eukaryotes, LRR domains developed into key recognition modules in many innate immune receptor classes. Due to the high sequence variability imposed by recognition specificity, precise repeat delineation is often difficult especially in plant NOD-like Receptors (NLRs) notorious for showing far larger irregularities. To address this problem, we introduce here LRRpredictor, a method based on an ensemble of estimators designed to better identify LRR motifs in general but particularly adapted for handling more irregular LRR environments, thus allowing to compensate for the scarcity of structural data on NLR proteins. The extrapolation capacity tested on a set of annotated LRR domains from six immune receptor classes shows the ability of LRRpredictor to recover all previously defined specific motif consensuses and to extend the LRR motif coverage over annotated LRR domains. This analysis confirms the increased variability of LRR motifs in plant and vertebrate NLRs when compared to extracellular receptors, consistent with previous studies. Hence, LRRpredictor is able to provide novel insights into the diversification of LRR domains and a robust support for structure-informed analyses of LRRs in immune receptor functioning.

scholarly journals Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu

2020 ◽  
Vol 48 (10) ◽  
pp. 5294-5305
Author(s):  
Shweta Karambelkar ◽  
Shubha Udupa ◽  
Vykuntham Naga Gowthami ◽  
Sharmila Giliyaru Ramachandra ◽  
Ganduri Swapna ◽  
...  
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Broad Host Range ◽  
Dna Modification ◽  
Bacteriophage Mu ◽  
Acetyl Coa ◽  
Protein Architecture ◽  
Iron Binding Protein ◽  
Free Radical Chemistry ◽  
Computational Analyses

Abstract The broad host range bacteriophage Mu employs a novel ‘methylcarbamoyl’ modification to protect its DNA from diverse restriction systems of its hosts. The DNA modification is catalyzed by a phage-encoded protein Mom, whose mechanism of action is a mystery. Here, we characterized the co-factor and metal-binding properties of Mom and provide a molecular mechanism to explain ‘methylcarbamoyl’ation of DNA by Mom. Computational analyses revealed a conserved GNAT (GCN5-related N-acetyltransferase) fold in Mom. We demonstrate that Mom binds to acetyl CoA and identify the active site. We discovered that Mom is an iron-binding protein, with loss of Fe2+/3+-binding associated with loss of DNA modification activity. The importance of Fe2+/3+ is highlighted by the colocalization of Fe2+/3+ with acetyl CoA within the Mom active site. Puzzlingly, acid-base mechanisms employed by >309,000 GNAT members identified so far, fail to support methylcarbamoylation of adenine using acetyl CoA. In contrast, free-radical chemistry catalyzed by transition metals like Fe2+/3+ can explain the seemingly challenging reaction, accomplished by collaboration between acetyl CoA and Fe2+/3+. Thus, binding to Fe2+/3+, a small but unprecedented step in the evolution of Mom, allows a giant chemical leap from ordinary acetylation to a novel methylcarbamoylation function, while conserving the overall protein architecture.

scholarly journals A protein architecture guided screen for modification dependent restriction endonucleases

2019 ◽  
Vol 47 (18) ◽  
pp. 9761-9776 ◽  
Author(s):  
Thomas Lutz ◽  
Kiersten Flodman ◽  
Alyssa Copelas ◽  
Honorata Czapinska ◽  
Megumu Mabuchi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Fusion Proteins ◽  
Dna Methyltransferase ◽  
Catalytic Domain ◽  
Dna Methyltransferases ◽  
Restriction Endonucleases ◽  
Endonuclease Activity ◽  
Protein Architecture ◽  
Escherichia Coli Cells ◽  
Dependent Activity

Abstract Modification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in Escherichia coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.

scholarly journals The architectural design of networks of protein domain architectures

2013 ◽  
Vol 9 (4) ◽  
pp. 20130268 ◽  
Author(s):  
Chia-Hsin Hsu ◽  
Chien-Kuo Chen ◽  
Ming-Jing Hwang
Keyword(s):  
Architectural Design ◽  
Molecular Form ◽  
Protein Domains ◽  
Single Domain ◽  
Protein Domain ◽  
Protein Architecture ◽  
Different Types ◽  
Protein Functions ◽  
Shed Light ◽  
Multiple Domain

Protein domain architectures (PDAs), in which single domains are linked to form multiple-domain proteins, are a major molecular form used by evolution for the diversification of protein functions. However, the design principles of PDAs remain largely uninvestigated. In this study, we constructed networks to connect domain architectures that had grown out from the same single domain for every single domain in the Pfam-A database and found that there are three main distinctive types of these networks, which suggests that evolution can exploit PDAs in three different ways. Further analysis showed that these three different types of PDA networks are each adopted by different types of protein domains, although many networks exhibit the characteristics of more than one of the three types. Our results shed light on nature's blueprint for protein architecture and provide a framework for understanding architectural design from a network perspective.

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