The protein structure initiative structural genomics knowledgebase

Berman, Helen M.; Westbrook, John D.; Gabanyi, Margaret; Tao, Wendy; Shah, Raship; Kouranov, Andrei; Schwede, Torsten; Arnold, Konstantin; Kiefer, Florian; Bordoli, Lorenza; Kopp, Jürgen; Podvinec, Michael; Adams, Paul D.; Carter, Lester G.; Minor, Władek; Nair, Rajesh; Baer, Joshua La

doi:10.1093/nar/gkn790

Cited by 98 publications

(91 citation statements)

References 23 publications

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“…As in the ligation pattern of EF hands, both carbonyl oxygen atoms of s3b's Glu901 provide two of the five equatorial ligation positions. The atoms describing the equatorial plane have an average deviation from planarity of 0.16 Å (see Table S2 in the supplemental material), which compares favorably to the 0.18-Å average deviations across calcium sites in calmodulin (PDB code 1OSA) (35). While calmodulin has a water molecule occupying one axial position, allowing for greater flexibility in the ligand position, both axial positions in s3b are supplied by amino acid side chains (Asn903 and Asp927).…”

Section: Resultsmentioning

confidence: 90%

Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum

et al. 2013

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Section: Resultsmentioning

confidence: 90%

Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum

et al. 2013

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“…PepcDB records status history, stop conditions, reusable text protocols and contact information collected from 15 SG centers in USA. The interested readers are directed to two recent articles by Helen Berman that introduce a wealth of resources concerning the SG initiative [41] and a knowledgebase developed by the Protein Structure Initiative [42].…”

Section: Databasesmentioning

confidence: 99%

Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis

Kurgan

Mizianty²

2009

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Structural genomics (SG) is an international effort that aims at solving three-dimensional shapes of important biological macro-molecules with primary focus on proteins. One of the main bottlenecks in SG is the ability to produce diffraction quality crystals for X-ray crystallography based protein structure determination. SG pipelines allow for certain flexibility in target selection which motivates development of insilico methods for sequence-based prediction/ assessment of the protein crystallization propensity. We overview existing SG databanks that are used to derive these predictive models and we discuss analytical results concerning protein sequence properties that were discovered to correlate with the ability to form crystals. We also contrast and empirically compare modern sequence-based predictors of crystallization propensity including OB-Score, ParCrys, XtalPred and CRYSTALP2. Our analysis shows that these methods provide useful and complimentary predictions. Although their average accuracy is similar at around 70%, we show that application of a simple majority-vote based ensemble improves accuracy to almost 74%. The best improvements are achieved by combining XtalPred with CRYSTALP2 while OB-Score and ParCrys methods overlap to a larger extend, although they still complement the other two predictors. We also demonstrate that 90% of the protein chains can be correctly predicted by at least one of these methods, which suggests that more accurate ensembles could be built in the future. We believe that current protein crystallization propensity predictors could provide useful input for the target selection procedures utilized by the SG centers.

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“…ac.uk/Tools/clustalw2/index.html). Structure-based alignments were performed using the "PSI-Nature Structural Genomics Knowledgebase" (Berman et al 2009). Protein data bank (PDB) searches were performed with distance matrix alignment (DALI) (Holm and Sander 1993).…”

Section: Methodsmentioning

confidence: 99%

The short form of the recombinant CAL-A-type lipase UM03410 from the smut fungus Ustilago maydis exhibits an inherent trans-fatty acid selectivity

Brundiek

Saß

Evitt

et al. 2012

Appl Microbiol Biotechnol

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The Ustilago maydis lipase UM03410 belongs to the mostly unexplored Candida antarctica lipase (CAL-A) subfamily. The two lipases with [corrected] the highest identity are a lipase from Sporisorium reilianum and the prototypic CAL-A. In contrast to the other CAL-A-type lipases, this hypothetical U. maydis lipase is annotated to possess a prolonged N-terminus of unknown function. Here, we show for the first time the recombinant expression of two versions of lipase UM03410: the full-length form (lipUMf) and an Nterminally truncated form (lipUMs). For comparison to the prototype, the expression of recombinant CAL-A in E. coli was investigated. Although both forms of lipase UM03410 could be expressed functionally in E. coli, the N-terminally truncated form (lipUMs) demonstrated significantly higher activities towards p-nitrophenyl esters. The functional expression of the N-terminally truncated lipase was further optimized by the appropriate choice of the E. coli strain, lowering the cultivation temperature to 20 °C and enrichment of the cultivation medium with glucose. Primary characteristics of the recombinant lipase are its pH optimum in the range of 6.5-7.0 and its temperature optimum at 55 °C. As is typical for lipases, lipUM03410 shows preference for long chain fatty acid esters with myristic acid ester (C14:0 ester) being the most preferred one.More importantly, lipUMs exhibits an inherent preference for C18:1Δ9 trans and C18:1Δ11 trans-fatty acid esters similar to CAL-A. Therefore, the short form of this U. maydis lipase is the only other currently known lipase with a distinct trans-fatty acid selectivity.

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The protein structure initiative structural genomics knowledgebase

Cited by 98 publications

References 23 publications

Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum

Structural Comparison of ColH and ColG Collagen-Binding Domains from Clostridium histolyticum

Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis

The short form of the recombinant CAL-A-type lipase UM03410 from the smut fungus Ustilago maydis exhibits an inherent trans-fatty acid selectivity

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