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Phosphorylation is critical to regulation of the eukaryotic cell cycle. Entry to mitosis is triggered by the cyclin-dependent kinase CDK1 (Cdc2), which is inactivated during the preceding S and G2 phases by phosphorylation of T14 and Y15. Two homologous kinases, Wee1, which phosphorylates Y15, and Myt1, which phosphorylates both T14 and Y15, mediate this inactivation. We have determined the crystal...
The open/closed transition in polymerases is a crucial event in DNA replication and transcription. We hypothesize that the residues that transmit the signal for the open/closed transition are also strongly conserved. To identify the dynamically relevant residues, we use an elastic network model of polymerases and probe the residue-specific response to a local perturbation. In a variety of DNA/RNA...
The binding of nonspecific DNA to the C-terminal negative regulatory domain (CTD) of p53 modulates its activity. The CTD is a natively unfolded region, which is subject to acetylation and phosphorylation at several residues as part of control. To measure the effect of covalent modification on binding to DNA, we synthesized a series of fluorescein-labeled CTD peptides with single and multiple acetylations...
Ferritins are known as important iron storage/detoxification proteins and are widely found in living organisms. This report details the 2.1 Å resolution native and 2.7 Å resolution iron bound structures of the ferritin from the hyperthermophilic Archaeon Archaeoglobus fulgidus, and represents the first structure of a ferritin from an archaeon, or a hyperthermophilic organism. The A. fulgidus ferritin...
Hsp90 is an abundant molecular chaperone involved in many biological systems. We report here the crystal structures of the unliganded and ADP bound fragments containing the N-terminal and middle domains of HtpG, an E. coli Hsp90. These domains are not connected through a flexible linker, as often portrayed in models, but are intimately associated with one another. The individual HtpG domains have...
The selectivity filter of potassium channels is the structural element directly responsible for the selective and rapid conduction of K + , whereas other parts of the protein are thought to function as a molecular gate that either permits or blocks the passage of ions. However, whether the selectivity filter itself also possesses the ability to play the role of a gate is an unresolved question...
We investigate the landscape of the internal free-energy of the 36 amino acid villin headpiece with a modified basin hopping method in the all-atom force field PFF01, which was previously used to predictively fold several helical proteins with atomic resolution. We identify near native conformations of the protein as the global optimum of the force field. More than half of the twenty best simulations...
The ubiquitin-associated (UBA) domain is one of the most frequently occurring motifs that recognize ubiquitin tags. Dsk2p, a UBA-containing protein from Saccharomyces cerevisiae, is involved in the ubiquitin-proteasome proteolytic pathway and has been implicated in spindle pole duplication. Here we present the solution structure of the UBA domain of Dsk2p (Dsk2 UBA ) in complex with ubiquitin...
The ABC ATPase RNase-L inhibitor (RLI) emerges as a key enzyme in ribosome biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. To help reveal the structural mechanism of RLI, we determined the Mg 2+ -ADP bound crystal structure of the twin cassette ATPase of P. furiosus RLI at 1.9 Å resolution and analyzed functional motifs in yeast in vivo. RLI shows...
In this issue, Shuman and coworkers use methylphosphonates as a nonnative substrate to investigate the mechanism of type IB topoisomerases (Tian et al., 2005, this issue of Structure). A surprising gain-of-function result was critical to assigning a catalytic role to an active site arginine.
Halorhodopsin is a light-driven chloride anion pump in which the trans→cis photoisomerization of a retinal chromophore triggers a photocyle resulting in the translocation of chloride across the plasma membrane. The mechanism of chloride transfer past the cis retinal is determined here by computing multiple pathways for this process. The calculations reveal two conditions of the valve mechanism. First,...
The helicase-primase interaction is a critical event in DNA replication and is mediated by a putative helicase-interaction domain within the primase. The solution structure of the helicase-interaction domain of DnaG reveals that it is made up of two independent subdomains: an N-terminal six-helix module and a C-terminal two-helix module that contains the residues of the primase previously identified...
Four conserved amino acids of type IB topoisomerases (Arg130, Lys167, Arg223, and His265 in vaccinia topoisomerase) catalyze the attack by tyrosine on the scissile phosphodiester to form a DNA-(3′-phosphotyrosyl)-enzyme intermediate. The mechanism entails general acid catalysis (by Lys167 and Arg130) and transition-state stabilization (via contact of His265 with the pro-Sp oxygen). Here we query the...
GTP hydrolysis by small GTP binding proteins of the Ras superfamily is a universal reaction that controls multiple cellular regulations. Its enzymic mechanism has been the subject of long-standing debates as to the existence/identity of the general base and the electronic nature of its transition state. Here we report the high-resolution crystal structure of a small GTP binding protein, Rab11, solved...
The single-chain twin-cassette ABC-ATPase RLI resembles other ABC nucleotide binding domains (Karcher et al., 2005, this issue of Structure), but seems to convey its mechanochemical ATP-dependent signals through a novel “hinge” region and/or an N-terminal FeS cluster, at sites where other ABC-ATPases have regulatory domains.
Oxygen is Nature’s perfect reagent. On one hand, it is potentially a very strong oxidant. On the other hand, this potential is caged because the two highest energy valence electrons of the O 2 molecule are unpaired. As a result, O 2 is relatively unreactive with most other molecules, as almost all of these have paired electrons. Consequently, by modulating the properties of the O ...
2-Oxoquinoline 8-monooxygenase is a Rieske non-heme iron oxygenase that catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline in the soil bacterium Pseudomonas putida 86. The crystal structure of the oxygenase component of 2-oxoquinoline 8-monooxygenase shows a ring-shaped, C3-symmetric arrangement in which the mononuclear Fe(II)...
The cyanobacterial circadian oscillator consists of three Kai proteins, KaiA, KaiB, and KaiC, in its oscillation feedback loop. Structural comparison reveals that the Kai system resembles the F1-ATPase system in which KaiC is equivalent to α 3 β 3 , KaiA to γδϵ, and KaiB to its inhibitory factor. It also suggests that there exists a possible haemagglutinin-like spring-loaded mechanism...
The secrets of ribosomally synthesized circular proteins are slowly revealed by gene sequencing and solution NMR studies of novel cyclotides and their precursors, as demonstrated by Mulvenna et al. (2005) in this issue of Structure.
Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were...
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