Abstract：
:ATP- and NAD(+)-dependent DNA ligases, ATP-dependent RNA ligases and GTP-dependent mRNA capping enzymes comprise a superfamily of proteins that catalyze nucleotidyl transfer to polynucleotide 5' ends via covalent enzyme-(lysyl-N)-NMP intermediates. The superfamily is defined by five peptide motifs that line the nucleotide-binding pocket and contribute amino acid sidechains essential for catalysis. Early crystal structures revealed a shared core tertiary structure for DNA ligases and capping enzymes, which are composed minimally of a nucleotidyltransferase domain fused to a distal OB-fold domain. Recent structures of viral and bacterial DNA ligases, and a fungal mRNA capping enzyme underscore how the substrate-binding and chemical steps of the ligation and capping pathways are coordinated with large rearrangements of the component protein domains and with remodeling of the atomic contacts between the enzyme and the nucleotide at the active site. The first crystal structure of an RNA ligase suggests that contemporary DNA ligases, RNA ligases and RNA capping enzymes evolved by fusion of ancillary effector domains to an ancestral catalytic module involved in RNA repair.
journal_name
Curr Opin Struct Bioljournal_title
Current opinion in structural biologyauthors
Shuman S,Lima CDdoi
10.1016/j.sbi.2004.10.006subject
Has Abstractpub_date
2004-12-01 00:00:00pages
757-64issue
6eissn
0959-440Xissn
1879-033Xpii
S0959-440X(04)00182-4journal_volume
14pub_type
杂志文章,评审abstract：:Solid-state NMR (ssNMR) offers insight into the formation of protein complexes and ligand binding for a large range of molecular sizes and binding affinities. Recent instrumental and methodological progress has enabled novel possibilities for using multi-dimensional ssNMR to study molecular 3D structures and interacti...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2006.08.003
更新日期：2006-10-01 00:00:00
abstract：:A novel ligand-binding domain, named the 'ACT domain', was recently identified by a PSI-BLAST search. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like betaalphabetabetaalphabeta topology. A pair of ACT domains form an eight-...
journal_title：Current opinion in structural biology
pub_type： 杂志文章
doi：10.1016/s0959-440x(01)00272-x
更新日期：2001-12-01 00:00:00
abstract：:The modulation of enzyme function is a key regulatory feature of biological systems. The ability to engineer synthetic enzymes that can be controlled by any arbitrary signal would enable a wide array of sensing applications and therapeutics and provide us with powerful tools for the basic study of biology. Here severa...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2009.04.007
更新日期：2009-08-01 00:00:00
abstract：:When a protein's function cannot be experimentally determined, it can often be inferred from sequence similarity. Should this process fail, analysis of the protein structure can provide functional clues or confirm tentative functional assignments inferred from the sequence. Many structure-based approaches exist (e.g. ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2005.04.003
更新日期：2005-06-01 00:00:00
abstract：:Pyrrolopyrimidine containing natural products are widely distributed in Nature. The biosynthesis of the 7-deazapurine moiety that is common to all pyrrolopyrimidines entails multiple steps, one of which is a complex radical-mediated ring contraction reaction catalyzed by CDG synthase. Herein we review the biosynthetic...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2015.11.005
更新日期：2015-12-01 00:00:00
abstract：:Phage display is the longest-standing platform among molecular display technologies. Recent developments have extended its utility to proteins that were previously recalcitrant to phage display. The technique has played a dominant role in forming the field of synthetic binding protein engineering, where novel interfac...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2007.08.007
更新日期：2007-08-01 00:00:00
abstract：:NMR relaxation experiments of isotopically labeled proteins provide a wealth of information on reorientational global and local dynamics on nanosecond and subnanosecond timescales for folded and nonfolded proteins in solution. Recent methodological advances in the interpretation of relaxation data have led to a better...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(03)00036-8
更新日期：2003-04-01 00:00:00
abstract：:RNA helicases are a large group of enzymes that function in virtually all aspects of RNA metabolism. Although RNA helicases share a highly conserved structure, different enzymes display a wide array of biochemical activities, including RNA duplex unwinding, protein displacement from RNA and strand annealing. Recent st...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2007.05.007
更新日期：2007-06-01 00:00:00
abstract：:The winged helix proteins constitute a subfamily within the large ensemble of helix-turn-helix proteins. Since the discovery of the winged helix/fork head motif in 1993, a large number of topologically related proteins with diverse biological functions have been characterized by X-ray crystallography and solution NMR ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(99)00057-3
更新日期：2000-02-01 00:00:00
abstract：:Mechanisms for making and breaking the heme b cofactor (heme) are more diverse than previously expected. Biosynthetic pathways have diverged at least twice along taxonomic lines, reflecting differences in membrane organization and O2 utilization among major groups of organisms. At least three families of heme degradas...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2019.01.006
更新日期：2019-12-01 00:00:00
abstract：:Large ribozymes fold on a 'glacial' timescale compared to the folding of their protein counterparts. The sluggish folding exhibited by large RNAs results from the formation of kinetically trapped, misfolded intermediates, which are nonessential features of the folding mechanism. Newly developed mutant ribozymes that a...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/S0959-440X(99)80045-1
更新日期：1999-06-01 00:00:00
abstract：:During protein evolution, novel domain arrangements are continuously formed. Rearrangements are important for the creation of molecular biodiversity and for functional molecular changes which underlie developmental shifts in the bauplan of organisms. Here we review the mechanisms by which new arrangements arise and th...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2013.02.012
更新日期：2013-06-01 00:00:00
abstract：:The eukaryotic genome is hierarchically packaged into chromatin in the nucleus. The organization and dynamics of 30-nm chromatin fibers, which is typically regarded as the secondary structure of chromatin, play a crucial role in regulating DNA accessibility for gene expression. Here we reviewed some recent progresses ...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2016.01.013
更新日期：2016-02-01 00:00:00
abstract：:Can a stereochemical recognition code explain sequence-specific protein-nucleic acid interactions? Whereas a code that is generally applicable to DNA-binding proteins of all known structural families is unattainable, the indications are that a code can describe at least some of the interactions of classical zinc finge...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(97)80015-2
更新日期：1997-02-01 00:00:00
abstract：:Condensation of DNA in the nucleosome takes advantage of its double-helical architecture. The DNA deforms at sites where the base pairs face the histone octamer. The largest so-called kink-and-slide deformations occur in the vicinity of arginines that penetrate the minor groove. Nucleosome structures formed from the 6...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2011.03.006
更新日期：2011-06-01 00:00:00
abstract：:Carbohydrate microarray technologies are new developments at the frontiers of glycomics. Results of 'proof of concept' experiments with carbohydrate-binding proteins of the immune system - antibodies, selectins, a cytokine and a chemokine - and several plant lectins indicate that microarrays of carbohydrates (glycocon...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2003.09.002
更新日期：2003-10-01 00:00:00
abstract：:Viruses with an icosahedrally symmetric protein capsid and a membrane infect hosts from all three domains of life. Similar architectural principles are shared by different viral families, as exemplified by double-stranded DNA viruses such as PRD1 and STIV. During virus assembly, the membrane lipids are selectively acq...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2007.03.005
更新日期：2007-04-01 00:00:00
abstract：:The encounter complex of two proteins is a dynamic intermediate state that guides proteins to their binding site, thus enhancing the rate of complex formation. It is particularly useful for complexes that must balance a biological requirement for high turnover with the need for specific binding, such as electron trans...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2013.07.009
更新日期：2013-12-01 00:00:00
abstract：:Functional conformational changes of proteins can facilitate numerous biological events in cells. The Markov state model (MSM) built from molecular dynamics simulations provide a powerful approach to study them. We here introduce a protocol that is tailor-made for constructing MSMs to study the functional conformation...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2020.10.005
更新日期：2020-10-27 00:00:00
abstract：:In vitro selection experiments are now routinely used to identify functional nucleic acid residues and structures, and have become a tool for studying molecular recognition, molecular biology, and molecular evolution. Technical innovations that have been made during the past year include the use of modified monomers t...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(96)80045-5
更新日期：1996-06-01 00:00:00
abstract：:2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concen...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2015.03.012
更新日期：2015-10-01 00:00:00
abstract：:X-ray radiation damage to cryocooled ( approximately 100 K) macromolecular crystals has emerged as a general problem, especially since the advent of third generation synchrotron undulator sources. Interest in understanding the physical and chemical phenomena behind the observed effects is growing rapidly. The specific...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2006.08.001
更新日期：2006-10-01 00:00:00
abstract：:For many protein families, such as serine proteinases or serine proteinase inhibitors, the family assignment predicts reactivity only in general terms. Both detailed specificity and quantitative reactivity are lacking. We believe that, for many such protein families, algorithms can be devised by defining the subset of...
journal_title：Current opinion in structural biology
pub_type： 杂志文章
doi：10.1016/s0959-440x(03)00013-7
更新日期：2003-02-01 00:00:00
abstract：:RNA-dependent RNA polymerases (RdRPs) play central roles in both transcription and viral genome replication. In picornaviruses, these functions are catalyzed by the virally encoded RdRP, termed 3D. Polymerase 3D also catalyzes the covalent linkage of UMP to a tyrosine on the small protein VPg. Uridylylated VPg then se...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2009.10.016
更新日期：2009-12-01 00:00:00
abstract：:Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape a...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2019.04.004
更新日期：2019-10-01 00:00:00
abstract：:Ising-like models have been remarkably successful in reproducing all the experimental data available on the equilibrium and kinetics of secondary structure formation in short peptides. Over the past two years, very similar models have been used to predict the folding of complete proteins, with encouraging results. Alt...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(00)00192-5
更新日期：2001-04-01 00:00:00
abstract：:There are now numerous examples of proteins that are unstructured or only partially structured under physiological conditions and yet are nevertheless functional. Such proteins are especially prevalent in eukaryotes. In many cases, intrinsically disordered proteins adopt folded structures upon binding to their biologi...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(02)00289-0
更新日期：2002-02-01 00:00:00
abstract：:Metal-binding sites have been engineered into both de novo designed and naturally occurring proteins. Although the redesign of existing metal-binding sites in naturally occurring proteins still offers the most promise for a successful design, the more challenging goal of engineering metal-binding sites in de novo desi...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/s0959-440x(97)80112-1
更新日期：1997-08-01 00:00:00
abstract：:The small multidrug resistance proteins constitute a family of bacterial antiporters that confer multidrug resistance by H(+)-linked drug efflux across the bacterial cytoplasmic membrane. The structure of EmrE, the family archetype, has been determined by electron crystallography and shows that EmrE in the membrane is...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2006.06.005
更新日期：2006-08-01 00:00:00
abstract：:Congenital disorders of glycosylation (CDG) are a group of diseases that affect glycoprotein biogenesis. Eighteen different types of CDG have been defined genetically. They result from deficiencies in either the biosynthesis of oligosaccharide precursors or specific steps of N-glycan assembly, resulting in the absence...
journal_title：Current opinion in structural biology
pub_type： 杂志文章,评审
doi：10.1016/j.sbi.2005.08.010
更新日期：2005-10-01 00:00:00
