Metalloproteomics: High-Throughput Structural and Functional Annotation of Proteins in Structural Genomics

Shi, Wuxian; Zhan, Changhong; Ignatov, Alexander; Manjasetty, Babu A.; Marinković, Nebojša; Sullivan, Michael; Huang, Raymond Y.; Chance, Mark R.

doi:10.1016/j.str.2005.07.014

Cited by 79 publications

(96 citation statements)

References 42 publications

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“…In the crystal, substitution of Cd 2ϩ ions for the natural Zn 2ϩ binding sites has been observed. Similar substitutions from the crystallization buffers have been previously reported (19). In VP9, all the natural Zn 2ϩ binding sites might be taken up by the Cd this fact, the NMR titration experiments with various divalent metal ions were carried out.…”

Section: Resultssupporting

confidence: 58%

“…Since there is no histidine and only one cysteine is present in the sequence of VP9, the observed coordinating side chains could be considered an unconventional binding site for Zn 2ϩ . Recently, Shi et al (19) reported a similar unconventional Zn 2ϩ binding site with His, Asp, and Glu. VP9 has identical coordinating side chains, except that histidine is replaced by cysteine.…”

Section: Resultsmentioning

confidence: 97%

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Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites

Liu¹,

Wu²,

Song

et al. 2006

J Virol

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White spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture. VP9, a full-length protein of WSSV, encoded by open reading frame wsv230, was identified for the first time in the infected Penaeus monodon shrimp tissues, gill, and stomach as a novel, nonstructural protein by Western blotting, mass spectrometry, and immunoelectron microscopy. Real-time reverse transcription-PCR demonstrated that the transcription of VP9 started from the early to the late stage of WSSV infection as a major mRNA species. The structure of full-length VP9 was determined by both X-ray and nuclear magnetic resonance (NMR) techniques. It is the first structure to be reported for WSSV proteins. The crystal structure of VP9 revealed a ferredoxin fold with divalent metal ion binding sites. Cadmium sulfate was found to be essential for crystallization. The Cd 2؉ ions were bound between the monomer interfaces of the homodimer. Various divalent metal ions have been titrated against VP9, and their interactions were analyzed using NMR spectroscopy. The titration data indicated that VP9 binds with both Zn 2؉ and Cd 2؉ . VP9 adopts a similar fold as the DNA binding domain of the papillomavirus E2 protein. Based on our present investigations, we hypothesize that VP9 might be involved in the transcriptional regulation of WSSV, a function similar to that of the E2 protein during papillomavirus infection of the host cells.Shrimp aquaculture has become an important industry worldwide during the last few decades. Intensive cultivation and massive worldwide trade of the shrimp and other aquaculture industries have led to the emergence and spread of numerous viral pathogens. Out of these viral pathogens, shrimp white spot syndrome virus (WSSV) is the most devastating to crustacean species. To date, there is no effective treatment available for WSSV infection.WSSV belongs to a new virus family, Nimaviridae, under a new genus, Whispovirus, which shares low sequence homology with other DNA viruses (16,24). WSSV is an enveloped virus with a 305-kb double-stranded circular DNA genome. Its genome was completely sequenced, with 180 predicted open reading frames (ORFs) (27). Most of these WSSV genes bear poor sequence homology with other known proteins, and thus the function of these genes cannot be predicted. However, a large amount of work has been carried out on the identification and characterization of WSSV structural proteins, including envelope and other capsid proteins. To date, a total of 39 structural proteins are known from WSSV (12, 23). A structure-based functional study is a promising approach to elucidate the function of such WSSV proteins. Besides the envelope and capsid proteins, nonstructural proteins are required for replication of the viral genome, production of the virus particle, and inhibition of the host cell functions. These proteins are therefore potential candidates for drug design and the development of vaccines.Here we report, for the first time, the identification of a novel, nonstructural WSSV protein, VP9. We have demon...

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Section: Resultssupporting

confidence: 58%

Section: Resultsmentioning

confidence: 97%

Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites

Liu¹,

Wu²,

Song

et al. 2006

J Virol

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“…1). One caveat might be the lack of complete proteome annotation; 60 to 65% of a given proteome can be structurally characterized with the SUPERFAMILY HMMs, yet the structural genomics initiative suggests that the nonannotated portions of proteomes have a similar proportion of metal-binding domains (24).…”

Section: Resultsmentioning

confidence: 99%

History of biological metal utilization inferred through phylogenomic analysis of protein structures

Dupont

Butcher

Valas³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

286

248

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The fundamental chemistry of trace elements dictates the molecular speciation and reactivity both within cells and the environment at large. Using protein structure and comparative genomics, we elucidate several major influences this chemistry has had upon biology. All of life exhibits the same proteome size-dependent scaling for the number of metal-binding proteins within a proteome. This fundamental evolutionary constant shows that the selection of one element occurs at the exclusion of another, with the eschewal of Fe for Zn and Ca being a defining feature of eukaryotic proteomes. Early life lacked both the structures required to control intracellular metal concentrations and the metal-binding proteins that catalyze electron transport and redox transformations. The development of protein structures for metal homeostasis coincided with the emergence of metal-specific structures, which predominantly bound metals abundant in the Archean ocean. Potentially, this promoted the diversification of emerging lineages of Archaea and Bacteria through the establishment of biogeochemical cycles. In contrast, structures binding Cu and Zn evolved much later, providing further evidence that environmental availability influenced the selection of the elements. The late evolving Zn-binding proteins are fundamental to eukaryotic cellular biology, and Zn bioavailability may have been a limiting factor in eukaryotic evolution. The results presented here provide an evolutionary timeline based on genomic characteristics, and key hypotheses can be tested by alternative geochemical methods.Archean-Proterozoic | biogeochemistry | bioinorganic chemistry | evolution | metal homeostasis M etalloproteins contain one or more ions of an inorganic element in their 3D structure and are said to comprise 30% of all proteins (1). Many biological pathways contain at least one metalloenzyme (2) and consequently require Mg, K, Ca, Fe, Mn, and Zn to sustain life (3). Other elements, like Cu, Mo, Ni, Se, and Co, are required by many-though not all-organismal lineages, and the utilization of trace elements varies greatly between species (3). The different elements have a range of affinities for most coordinating environments in the order Mg +2 /Ca +2 < Mn +2 < Fe +2 < Co +2 < Ni +2 < Cu +2 ∼Zn +2 , an equilibrium series known as the Irving-Williams Series (4). This array of outer-sphere chemistry provides significant catalytic diversity, yet has consequences for both biological and environmental chemistry. Within the cell, metals compete for protein binding sites; hence, extensive protein networks involving transporters and metalsensing regulatory proteins are required to maintain the proper subcellular concentrations of each element, and in some cases directly shuttle each metal to its requisite metalloprotein in the proper cellular compartment (1, 5, 6). It has been hypothesized that the establishment of a metal homeostasis system is required for distinct phylotypes of cells to develop (7).Environmentally, for similar fundamental chemical reasons, the...

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“…Bertini et al proposed an approach taking advantage of known consensus sequences, i.e., taking into account the nature and spacing of amino acids present in the metal-binding region; the distribution of iron-, copper-, and zinc-binding proteins in several archaea, bacteria, and eukaryotes was thus described [65]. The bioinformatic analysis of the protein sequence (by correlation with the relevant gene) allows the finding of the conserved metal-binding motifs and provides important clues to function and metal site structure [68]. This approach is critically dependent on the availability of consensus sequences for the binding of different metals.…”

Section: Bioinformatics and Prediction Of The Metal-binding Patternsmentioning

confidence: 99%

Metallomics: Guidelines for terminology and critical evaluation of analytical chemistry approaches (IUPAC Technical Report)

Łobiński

Becker

Haraguchi

et al. 2010

Pure and Applied Chemistry

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Definitions for the terms "metallome" and "metallomics" are proposed. The state of the art of analytical techniques and methods for systematic studies of metal content, speciation, localization, and use in biological systems is briefly summarized and critically evaluated.Keywords: metals; metabolomics; metallomics; proteomics; speciation. RATIONALE AND HISTORY OF THE USE OF THE TERMS REGARDING THE METAL-RELATED -OMICSThe knowledge of the complete genetic blueprint of an increasing number of organisms has resulted in efforts aimed at the global analysis and functional study of a particular class of components of a living organism and the emergence of different "-omics". The concepts of genomics (the study of genes and their function) and proteomics (the study of the set of proteins produced by an organism, their localization, structure, stability, and interaction) have become part of the everyday language of life sciences [1,2].Metal ions are a vital component of the chemistry of life [3]. One-third of all proteins is believed to require a metal cofactor, such as copper, iron, zinc, or molybdenum [4], delivered as a simple or complex ion or a metal-containing compound (e.g., methylcobalamin). The intracellular concentration of several metals, their distribution among the various cell compartments, and their incorporation in metallo proteins are tightly controlled [5]. The understanding of mechanisms by which a metal is sensed, stored, or incorporated as a cofactor requires, in addition to the identification of metalloproteins, the characterization of the pool of non-protein molecules (products of enzymatic or biochemical reactions) interacting with metal ions or of metabolites of exogenous metallocompounds, such as metallodrugs. A systematic approach to the study of metal content, speciation, localization, and use in biological systems is becoming increasingly important [6].

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Metalloproteomics: High-Throughput Structural and Functional Annotation of Proteins in Structural Genomics

Cited by 79 publications

References 42 publications

Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites

Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites

History of biological metal utilization inferred through phylogenomic analysis of protein structures

Metallomics: Guidelines for terminology and critical evaluation of analytical chemistry approaches (IUPAC Technical Report)

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