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Yonglin Hu

Bio: Yonglin Hu is an academic researcher from California Institute of Technology. The author has contributed to research in topics: Pyrococcus furiosus & Molybdenum cofactor. The author has an hindex of 4, co-authored 4 publications receiving 329 citations.

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TL;DR: The structures of the oxidized and reduced forms of SOR suggest a mechanism by which superoxide accessibility may be controlled and define a possible binding site for rubredoxin, the likely physiological electron donor to SOR.
Abstract: Superoxide reductase (SOR) is a blue non-heme iron protein that functions in anaerobic microbes as a defense mechanism against reactive oxygen species by catalyzing the reduction of superoxide to hydrogen peroxide [Jenney, F. E., Jr., Verhagen, M. F. J. M., Cui, X., and Adams, M. W. W. (1999) Science 286, 306−309]. Crystal structures of SOR from the hyperthermophilic archaeon Pyrococcus furiosus have been determined in the oxidized and reduced forms to resolutions of 1.7 and 2.0 A, respectively. SOR forms a homotetramer, with each subunit adopting an immunoglobulin-like β-barrel fold that coordinates a mononuclear, non-heme iron center. The protein fold and metal center are similar to those observed previously for the homologous protein desulfoferrodoxin from Desulfovibrio desulfuricans [Coelho, A. V., Matias, P., Fulop, V., Thompson, A., Gonzalez, A., and Carrondo, M. A. (1997) J. Bioinorg. Chem. 2, 680−689]. Each iron is coordinated to imidazole nitrogens of four histidines in a planar arrangement, with a cysteine ligand occupying an axial position normal to this plane. In two of the subunits of the oxidized structure, a glutamate carboxylate serves as the sixth ligand to form an overall six-coordinate, octahedral coordinate environment. In the remaining two subunits, the sixth coordination site is either vacant or occupied by solvent molecules. The iron centers in all four subunits of the reduced structure exhibit pentacoordination. The structures of the oxidized and reduced forms of SOR suggest a mechanism by which superoxide accessibility may be controlled and define a possible binding site for rubredoxin, the likely physiological electron donor to SOR.

140 citations

Journal ArticleDOI
TL;DR: Crystal structures of formaldehyde ferredoxin oxidoreductase (FOR), a tungstopterin-containing protein from the hyperthermophilic archaeon Pyrococcus furiosus, have been determined in the native state and as a complex with the inhibitor glutarate at 1.85 A and 2.4 A resolution.

102 citations

Journal ArticleDOI
TL;DR: The specificity exhibited by the molybdate binding protein ModA for molyBdate and tungstate reflects the size and ligands of the anion binding pocket.
Abstract: The specificity exhibited by the molybdate binding protein ModA for molybdate and tungstate reflects the size and ligands of the anion binding pocket.

71 citations

Journal ArticleDOI
Abstract: The molybdenum cofactor (Moco) has been found to be associated with a diverse set of redox enzymes and contains a mononuclear molybdenum or tungsten ion co-ordinated by the dithiolene sulfurs of one or two molybdopterin {a pterin [2-amino-4(1H)-pteridinone] derivative} ligands. The remaining co-ordination sites on the metal are occupied by non-protein oxygen or sulfur species and, occasionally, amino acid side chains. The molybdopterin ligand can exhibit oxidation-state-dependent changes in structure and metal co-ordination, and may also interact with other redox groups in the enzyme. These observations suggest that the molybdopterin may participate in the various electron-transfer reactions associated with the catalytic mechanism of Moco containing enzymes.

27 citations


Cited by
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TL;DR: The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions.
Abstract: Summary: ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.

1,194 citations

Journal ArticleDOI
TL;DR: The SORs and three very different types of SOD enzymes are redox-active metalloenzymes that have evolved entirely independently from one another for the purpose of lowering superoxide concentrations, suggesting that, from the start of the rise of O2 on Earth, the chemistry of superoxide has been an important factor during evolution.
Abstract: Superoxide, O2•–, is formed in all living organisms that come in contact with air, and, depending upon its biological context, it may act as a signaling agent, a toxic species, or a harmless intermediate that decomposes spontaneously Its levels are limited in vivo by two different types of enzymes, superoxide reductase (SOR) and superoxide dismutase (SOD) Although superoxide has long been an important factor in evolution, it was not so when life first emerged on Earth at least 35 billion years ago At that time, the early biosphere was highly reducing and lacking in any significant concentrations of dioxygen (O2), very different from what it is today Consequently, there was little or no O2•– and therefore no reason for SOR or SOD enzymes to evolve Instead, the history of biological O2•– probably commences somewhere around 24 billion years ago, when the biosphere started to experience what has been termed the “Great Oxidation Event”, a transformation driven by the increase in O2 levels, formed by cyanobacteria as a product of oxygenic photosynthesis1 The rise of O2 on Earth caused a reshaping of existing metabolic pathways, and it triggered the development of new ones2 Its appearance led to the formation of the so-called “reactive oxygen species” (ROS), for example, superoxide, hydrogen peroxide, and hydroxyl radical, and to a need for antioxidant enzymes and other antioxidant systems to protect against the growing levels of oxidative damage to living systems Dioxygen is a powerful four-electron oxidizing agent, and the product of this reduction is water 1 When O2 is reduced in four sequential one-electron steps, the intermediates formed are the three major ROS, that is, O2•–, H2O2, and HO• 2 3 4 5 Each of these intermediates is a potent oxidizing agent The consequences of their presence to early life must have been an enormous evolutionary challenge In the case of superoxide, we find the SOD and SOR enzymes to be widely distributed throughout current living organisms, both aerobic and anaerobic, suggesting that, from the start of the rise of O2 on Earth, the chemistry of superoxide has been an important factor during evolution The SORs and three very different types of SOD enzymes are redox-active metalloenzymes that have evolved entirely independently from one another for the purpose of lowering superoxide concentrations SORs catalyze the one-electron reduction of O2•– to give H2O2, a reaction requiring two protons per superoxide reacted as well as an external reductant to provide the electron (eq 6) SODs catalyze the disproportionation of superoxide to give O2 and H2O2, a reaction requiring one proton per superoxide reacted, but no external reductant (eq 7) 6 7 All of the SOR enzymes contain only iron, while the three types of SODs are the nickel-containing SODs (NiSOD), the iron- or manganese-containing SODs (FeSOD and MnSOD), and the copper- and zinc-containing SODs (CuZnSOD) Although the structures and other properties of these four types of metalloenzymes are quite different, they all share several characteristics, including the ability to react rapidly and selectively with the small anionic substrate O2•– Consequently, there are some striking similarities between these otherwise dissimilar enzymes, many of which can be explained by considering the nature of the chemical reactivity of O2•– (see below) Numerous valuable reviews describing the SOD and SOR enzymes have appeared over the years, but few have covered and compared all four classes of these enzymes, as we attempt to do here Thus, the purpose of this Review is to describe, compare, and contrast the properties of the SOR and the four SOD enzymes; to summarize what is known about their evolutionary pathways; and to analyze the properties of these enzymes in light of what is known of the inherent chemical reactivity of superoxide

641 citations

Journal ArticleDOI
TL;DR: The SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving to create an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering.
Abstract: We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

604 citations

Journal ArticleDOI
TL;DR: Metal homeostasis is governed by the formation of specific protein-metal coordination complexes used to effect uptake, efflux, intracellular trafficking within compartments, and storage, and is the focus of this review.
Abstract: The transition or d-block metal ions manganese, iron, cobalt, nickel, copper, zinc, and to a more specialized degree, molybdenum, tungsten and vanadium, have been shown to be important for biological systems. These metal ions are ubiquitously found in nature, nearly exclusively as constituents of proteins.1 The unique properties of metal ions have been exploited by nature to perform a wide range of tasks. These include roles as structural components of biomolecules, as signaling molecules, as catalytic cofactors in reversible oxidation-reduction and hydrolytic reactions, and in structural rearrangements of organic molecules and electron transfer chemistry.1 Indeed, metal ions play critical roles in the cell that cannot be performed by any other entity, and are therefore essential for all of life. However, an individual metal ion is capable of performing only one or a few of these functions, but certainly not all; as a result, nature has evolved mechanisms to effectively distinguish one metal from another. The coordination chemistry of metal ion-protein complexes is fundamental to this biological discrimination, and is largely the focus of this review. 1.1. Metal Ion Homeostasis Extensive regulatory and protein-coding machinery is devoted to maintaining the “homeostasis” of biologically required metal ions and underscores the essentiality of this process for cell viability. Homeostasis is defined as the maintenance of an optimal bioavailable concentration, mediated by the balancing of metal uptake and intracellular trafficking with efflux/storage processes so that the needs of the cell for that metal ion is met, i.e., the “right” metal is inserted into the “right” macromolecule at the appropriate time.2,3 Just as a scarcity of a particular metal ion induces a stress response that can lead to reprogramming of cellular metabolism to minimize the consequences of depletion of a particular metal ion, e.g., zinc in ribosome biogenesis4 or Cu vs. Fe in photosynthesis by Synechocystis,5 too much of the same metal ion can also be toxic to a cell or organism. Metal homeostasis is governed by the formation of specific protein-metal coordination complexes used to effect uptake, efflux, intracellular trafficking within compartments, and storage (Figure 1). How metal ions move to and from their target destinations in the active site of a metalloenzyme or as a structural component of biomolecules also contributes to intracellular metal homeostasis (Figure 1). Metal transporters move metal ions or small molecule-metal chelates across otherwise impermeable barriers in a directional fashion, and most of these are integral membrane proteins embedded in the inner or plasma membrane (Figure 1). Specialized protein chelators designated metallochaperones traffic metals within a particular cellular compartment, e.g., the periplasm or the cytosol, and function to “hold” the metal in such a way that it can be readily transferred to an appropriate acceptor protein. This intermolecular transfer is known or is projected to occur through transiently formed, specific protein-protein complexes that mediate coordinated intermolecular metal ligand exchange. Metallochaperones have been described for copper,6-9 nickel10 and iron-sulfur protein biogenesis,11 and recent work suggests that the periplasmic Zn(II) binding protein, YodA, has characteristics consistent with a role as a zinc chaperone in E. coli (Figure 1).12 Salient features of these chaperones are discussed in more detail in the context of acquisition and efflux of individual metal ions (Section 2). Finally, specialized transcriptional regulatory proteins, termed metalloregulatory or metal sensor proteins, control the expression of genes encoding these proteins that establish metal homeostasis in response to either metal deprivation or overload (Section 3). Figure 1 Schematic metal homeostasis models for iron, zinc and manganese, copper, nickel and cobalt, shown specifically in gram-negative bacteria. Homeostasis of molybdate and tungstate oxyanions are not shown, due primarily to a lack of knowledge of these systems, ... A hypothesis that emerges is that in order to effect the cellular homeostasis of a particular metal ion, each component of the homeostasis machinery (Figure 1) must be selective for that metal ion under the prevailing conditions, to the exclusion of all others.13 Furthermore, individual systems must be “tuned” such that the affinity or sensitivity of each component is well-matched, either to coordinate gene expression by pairs of metal sensor proteins that coordinately shut off uptake and up-regulate efflux or detoxification systems, or to facilitate vectorial transport from metal donor to metal acceptor target protein in a metal trafficking pathway in the cell (Figure 1).14-16

521 citations