The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource

Gifford, Lida K.; Carter, Lester G.; Gabanyi, Margaret; Berman, Helen M.; Adams, Paul D.

doi:10.1007/s10969-012-9133-7

Cited by 20 publications

(17 citation statements)

References 33 publications

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“…Assuming current trends, ∼55% coverage will be achieved within 15 y, a level considered sufficient to fully characterize the metabolic network of an organism. These efforts are complemented by nine centers focused on membrane protein structure determination, as well as additional resources for data tracking and dissemination (www.sbkb.org) (13) and a materials repository (14).…”

Section: Significancementioning

confidence: 99%

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

Khafizov

Madrid-Aliste

Almo

et al. 2014

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

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The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins—including proteins for which reliable homology models can be generated—on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long.

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Section: Significancementioning

confidence: 99%

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

Khafizov

Madrid-Aliste

Almo

et al. 2014

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

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“…An important resource presenting SG data is the PSI Structural Biology Knowledgebase [55,69] (SBKB; http://sbkb.org), which makes available protocols created for the purpose of protein structure and function determination, papers highlighting new findings in structural biology work, and recent technology or methodology developments created by SG programs. Recently, a significant fraction of the X-ray diffraction data collected by the US-based structural genomics programs has been made publicly available by the new Integrated Resource for Reproducibility in Macromolecular Crystallography (http://proteindiffraction.org).…”

Section: Data Databanks Databases and Other Resourcesmentioning

confidence: 99%

The impact of structural genomics: the first quindecennial

Grabowski

Niedzialkowska

Zimmerman

et al. 2016

J Struct Funct Genomics

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The period 2000–2015 brought the advent of high-throughput approaches to protein structure determination. With the overall funding on the order of $2 billion (in 2010 dollars), the structural genomics (SG) consortia established worldwide have developed pipelines for target selection, protein production, sample preparation, crystallization, and structure determination by X-ray crystallography and NMR. These efforts resulted in the determination of over 13,500 protein structures, mostly from unique protein families, and increased the structural coverage of the expanding protein universe. SG programs contributed over 4,400 publications to the scientific literature. The NIH-funded Protein Structure Initiatives (PSI) alone have produced over 2,000 scientific publications, which to date have attracted more than 93,000 citations. Software and database developments that were necessary to handle high-throughput structure determination workflows have led to structures of better quality and improved integrity of the associated data. Organized and accessible data have a positive impact on the reproducibility of scientific experiments. Most of the experimental data generated by the SG centers are freely available to the community and has been utilized by scientists in various fields of research. SG projects have created, improved, streamlined, and validated many protocols for protein production and crystallization, data collection, and functional analysis, significantly benefiting biological and biomedical research.

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“…Many of these gene products could represent new “parts” for natural host metabolic diversification or metabolic engineering (Hanson et al, 2010). Systematic approaches to illuminate the structure and function of unknown proteins have been implemented, such as in the Protein Structure Initiative (Gifford et al, 2012) and the Enzyme Function Initiative (Gerlt et al, 2011). Using protein structure as a guide combined with genome context, computational predictions, and experimental data provide powerful platforms for the discovery of new enzymes (Bastard et al, 2014; Zhao et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

An Atypical Orphan Carbohydrate-NRPS Genomic Island Encodes a Novel Lytic Transglycosylase

Guo

Crawford

2014

Chemistry & Biology

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SUMMARY Microbial genome sequencing platforms have produced a deluge of orphan biosynthetic pathways suspected of biosynthesizing new small molecules with pharmacological relevance. Genome synteny analysis provides an assessment of genomic island content, which is enriched in natural product gene clusters. Here we identified an atypical orphan carbohydrate-nonribosomal peptide synthetase (NRPS) genomic island in Photorhabdus luminescens using genome synteny analysis. Heterologous expression of the pathway led to the characterization of five new oligosaccharide metabolites with lysozyme inhibitory activities. The oligosaccharides harbor a 1,6-anhydro-β-D-N-acetyl-glucosamine (Glc-NAc) moiety, a rare structural feature for natural products. Gene deletion analysis and biochemical reconstruction of oligosaccharide production led to the discovery that a hypothetical protein in the pathway is a novel lytic transglycosylase responsible for bicyclic sugar formation. The example presented here supports a notion where targeting select genomic islands with a reduced reliance on known protein homologies could enhance the discovery of new metabolic chemistry and biology.

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The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource

Cited by 20 publications

References 33 publications

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

The impact of structural genomics: the first quindecennial

An Atypical Orphan Carbohydrate-NRPS Genomic Island Encodes a Novel Lytic Transglycosylase

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