Abstract：
BACKGROUND:The N-end rule pathway is a part of the ubiquitin-dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-zinc-stabilized heart-shaped fold. RESULTS:Using sequence and structure analysis we argue that the UBR-box fold emerged from a binuclear RING-like treble clef zinc finger. The RING-like core is preserved in the UBR-box and the metal-chelating motifs display significant sequence and structural similarity to B-box and ZZ domains. UBR-box domains retrieved in our analysis co-occur with a variety of other protein domains, suggestive of its involvement in diverse biological roles. The UBR-box is a unique family of RING-like treble clefs as it displays a distinct circular permutation at the zinc-knuckle of the first zinc-binding site unlike other documented permutations of the RING-like domains which occur at the second zinc-binding site. The circular permutation of the RING-like treble clef scaffold has possibly aided the gain of a novel and relatively deep cleft suited for binding N-degrons. The N- and C-terminal extensions to the circularly permuted RING-like region bind a third zinc ion, which likely provides additional stability to the domain by keeping the two halves of the permuted zinc-knuckle together. CONCLUSIONS:Structural modifications and extensions to the RING-like core have resulted in a novel UBR-box fold, which can recognize and target the type 1 N-degron containing proteins for ubiquitin-mediated proteolysis. The UBR-box appears to have emerged during the expansion of ubiquitin system pathway-related functions in eukaryotes, but is also likely to have other non-N-recognin functions as well.
journal_name
Biol Directjournal_title
Biology directauthors
Kaur G,Subramanian Sdoi
10.1186/s13062-015-0066-5subject
Has Abstractpub_date
2015-07-17 00:00:00pages
36issn
1745-6150pii
10.1186/s13062-015-0066-5journal_volume
10pub_type
杂志文章相关文献
Biology Direct文献大全abstract：BACKGROUND:Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metageno...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-018-0225-6
更新日期：2018-10-12 00:00:00
abstract：BACKGROUND:It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-5-64
更新日期：2010-11-18 00:00:00
abstract：BACKGROUND:Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches--the examination of similarities to known disease genes and/or the evaluation of functional annotation of...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-6-30
更新日期：2011-06-13 00:00:00
abstract：BACKGROUND:The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, is one of the most important events in the evolution of eukaryotic cells. How proteins were selected for im...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-020-00263-6
更新日期：2020-04-28 00:00:00
abstract：BACKGROUND:Recent studies suggest that gene expression profiles are a promising alternative for clinical cancer classification. One major problem in applying DNA microarrays for classification is the dimension of obtained data sets. In this paper we propose a multiclass gene selection method based on Partial Least Squa...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-7-33
更新日期：2012-10-02 00:00:00
abstract：:Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses o...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-015-0047-8
更新日期：2015-03-29 00:00:00
abstract：BACKGROUND:The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequen...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-016-0120-y
更新日期：2016-04-07 00:00:00
abstract：:It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate descript...
journal_title：Biology direct
pub_type： 历史文章,杂志文章,评审
doi：10.1186/1745-6150-4-43
更新日期：2009-11-16 00:00:00
abstract：BACKGROUND:Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is ...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-018-0209-6
更新日期：2018-05-09 00:00:00
abstract：BACKGROUND:Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key proteins maintaining function and stability of the network. Therefore, studying protein-protein complexes ...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-6-49
更新日期：2011-10-05 00:00:00
abstract：BACKGROUND:The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets p...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-020-00287-y
更新日期：2020-12-10 00:00:00
abstract：BACKGROUND:BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-7-12
更新日期：2012-04-17 00:00:00
abstract：BACKGROUND:In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review t...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-6-7
更新日期：2011-02-08 00:00:00
abstract：BACKGROUND:One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. RESULTS:In order to address this problem, we developed...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-016-0118-5
更新日期：2016-03-25 00:00:00
abstract：BACKGROUND:The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-8-17
更新日期：2013-07-08 00:00:00
abstract：BACKGROUND:Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population d...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-9-23
更新日期：2014-11-18 00:00:00
abstract：BACKGROUND:The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in v...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-4-19
更新日期：2009-06-03 00:00:00
abstract：:LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are capable of synthesizing DNA on their own RNA templates by harnessing reverse transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their RT are found to globally influence gene expression profiles, differentiati...
journal_title：Biology direct
pub_type： 杂志文章,评审
doi：10.1186/1745-6150-8-22
更新日期：2013-09-13 00:00:00
abstract：BACKGROUND:The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distr...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-7-32
更新日期：2012-09-26 00:00:00
abstract：:In this article, I review the results of studies on the origin of life distinct from the popular RNA world hypothesis. The alternate scenario postulates the origin of the first bimolecular genetic system (a polynucleotide gene and a polypeptide processive polymerase) with simultaneous replication and translation and i...
journal_title：Biology direct
pub_type： 杂志文章,评审
doi：10.1186/s13062-015-0096-z
更新日期：2015-11-26 00:00:00
abstract：BACKGROUND:Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS:Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the bet...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-2-4
更新日期：2007-01-24 00:00:00
abstract：BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, p...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-016-0159-9
更新日期：2016-10-21 00:00:00
abstract：UNLABELLED:Recently Mycobacterium tuberculosis was shown to possess a novel protein modification, in which a small protein Pup is conjugated to the epsilon-amino groups of lysines in target proteins. Analogous to ubiquitin modification in eukaryotes, this remarkable modification recruits proteins for degradation via ar...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-3-45
更新日期：2008-11-03 00:00:00
abstract：UNLABELLED:Pseudogenes arise from the decay of gene copies following either RNA-mediated duplication (processed pseudogenes) or DNA-mediated duplication (nonprocessed pseudogenes). Here, we show that long protein-coding genes tend to produce more nonprocessed pseudogenes than short genes, whereas the opposite is true f...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-4-38
更新日期：2009-10-06 00:00:00
abstract：BACKGROUND:While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria,...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-1-28
更新日期：2006-09-13 00:00:00
abstract：BACKGROUND:The gammadelta T cells serve as early immune defense against certain encountered microbes. Only a few gammadelta T cell-recognized ligands from microbial antigens have been identified so far and the mechanisms by which gammadelta T cells recognize these ligands remain unknown. Here we explored the mechanism ...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-4-47
更新日期：2009-12-01 00:00:00
abstract：BACKGROUND:The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenerge...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/s13062-018-0221-x
更新日期：2018-10-03 00:00:00
abstract：:Chron's Disease is a chronic inflammatory intestinal disease, first described at the beginning of the last century. The disease is characterized by the alternation of periods of flares and remissions influenced by a complex pathogenesis in which inflammation plays a key role. Crohn's disease evolution is mediated by a...
journal_title：Biology direct
pub_type： 杂志文章,评审
doi：10.1186/s13062-020-00280-5
更新日期：2020-11-07 00:00:00
abstract：BACKGROUND:Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive families or families of repeats. Recently, we proposed that families of TEs originate in small populati...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-7-36
更新日期：2012-10-25 00:00:00
abstract：BACKGROUND:Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. ...
journal_title：Biology direct
pub_type： 杂志文章
doi：10.1186/1745-6150-7-1
更新日期：2012-01-05 00:00:00
