{"id":4234,"date":"2015-06-18T10:25:52","date_gmt":"2015-06-18T08:25:52","guid":{"rendered":"http:\/\/news.embl.de\/?p=4234"},"modified":"2024-11-29T16:52:58","modified_gmt":"2024-11-29T15:52:58","slug":"1506-enzyme","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/","title":{"rendered":"The curious case of the bi-specific enzyme"},"content":{"rendered":"\n

Curiosity created the crystal<\/h3>\n\n\n\n

\u201cWhen I first learnt about the possibility of sending my samples to EMBL Hamburg, I was curious to give it a try,\u201d Rentmeister says, recalling how she first heard about the services offered by the SPC facility<\/a>. She wanted to learn more about the molecular structure of an enzyme found in cyanobacteria \u2013 a group of photosynthetic bacteria that can cause toxic blooms in lakes in the summer.<\/p>\n\n\n\n

Specifically, Rentmeister was interested in one part of the multi-modular enzyme known as a nonribosomal peptide synthetase (NRPS). \u201cNRPS enzymes are like assembly lines,\u201d she explains. \u201cThey are made up of multiple domains, all needed to assemble a peptide chain: the first domain picks up an amino acid, a second hands it to a third domain that binds the amino acid to the next to form a peptide chain.\u201d The first domain is usually specific to a single amino acid \u2013 only able to bind to one of the 20 common amino acids. \u201cPeople have been bothered by this specificity for a long time,\u201d says Rentmeister, \u201cThere are already several crystals structures of similar enzymes that show the binding \u2018pocket\u2019 for the amino acid.\u201d<\/p>\n\n\n\n

It\u2019s intriguing that an enzyme can be specific to both Arginine and Tyrosine \u2013 structurally two very distinct amino acids.<\/p><\/blockquote>\n\n\n\n

\u201cScientists have generated a specificity code based on the residues found on the inside surface of this pocket, enabling us to predict which amino acid might bind with the enzyme,\u201d continues Rentmeister. But this code is not 100% reliable and Rentmeister\u2019s co-author, Guntram Christiansen from the University of Innsbruck, claimed to have found a domain that recognises not one, but two amino acids. \u201cIt\u2019s intriguing that an enzyme can be specific to both Arginine and Tyrosine \u2013 structurally two very distinct amino acids,\u201d Rentmeister explains. \u201cWe were puzzled: no one could explain how this was possible \u2013 maybe there is a second separate binding pocket?\u201d Hence, her expedition into the world of structural biology, and to Hamburg to try to crystallise the curious enzyme and study its molecular structure on the EMBL beamlines at PETRA III<\/a>.<\/p>\n\n\n\n

\"1506-spc-samples2\"
Algal bloom formed by the cyanobacterium Microcystis in a pond in Bavaria, Germany. PHOTO: Rainer Kurmayer, University of Innsbruck.<\/figcaption><\/figure>\n\n\n\n

A re-think<\/h3>\n\n\n\n

Rentmeister\u2019s initial excitement was, however, short lived: \u201cAfter a round of unsuccessful crystallisation experiments in 2011, I thought \u2013 ok, it was a nice experience, but no result.\u201d Fortunately, at this time, SPC facility manager Rob Meijers started to offer a follow-up service to users who had failed to crystalise their proteins \u2013 people like Rentmeister. Meijers got in contact to suggest another round of experiments focusing on quality control and optimisation.<\/p>\n\n\n\n

Crystallising a protein is not as easy as producing crystals from a solution of kitchen salt.<\/p><\/blockquote>\n\n\n\n

\u201cCrystallising a protein is not as easy as producing crystals from a solution of kitchen salt – that\u2019s why we decided to set up a service to help non-experts get the most out of their samples,\u201d explains Meijers. \u201cNow when we receive a sample, like this enzyme, we set up hundreds of experiments each a few nano-milliliters in volume with varying concentrations of buffers and salts to try to find the best conditions for crystallisation.\u201d<\/p>\n\n\n\n

\"1506-spc-samples1\"
Cultures of a cyanobacterium grown under different nutrient concentrations to investigate regulation of toxin production. PHOTO: Rainer Kurmayer, University of Innsbruck.<\/figcaption><\/figure>\n\n\n\n

Soaking it in<\/h3>\n\n\n\n

\u201cBased on Rob\u2019s feedback we re-designed the experiment and got nice crystals,\u201d says Rentmeister. But, once again, enthusiasm was fleeting: the data from the beamline experiments did not allow the researchers to completely observe the part of the enzyme of interest \u2013 the part involved in amino acid specificity. Not to be beaten, Meijers\u2019 then-PhD student Heidi Kaljunen started a series of \u2018soaking\u2019 experiments, drenching the crystals in solutions containing amino acid molecules so that the enzymes would bind to their specific amino acids, Arginine and Tyrosine. At last, the team succeeded in crystalising and resolving structures of the enzyme in combination with the two amino acids. Moreover, the structures showed that, once the amino acid has taken its place, the pocket is sealed off so that the amino acid can be bound to the peptide chain.<\/p>\n\n\n\n

Contrary to Rentmeister\u2019s initial theory \u2013 that the enzyme might have a second binding site \u2013 both amino acids are seen using the same pocket. \u201cThe most amazing thing is that if you superimpose the structures of the two amino acids bound to the enzyme, you see how the amino acid Arginine snuggles into the binding pocket pretending to be a Tyrosine,\u201d she says. The crystal structures show how one end of the Arginine molecule curls in on itself, mimicking the structure of Tyrosine. \u201cIt was both interesting and disappointing, because the answer was so simple and logical!\u201d<\/p>\n\n\n\n

\"1506-spc-crystals-new\"
Crystals of the NRPS enzyme, approximatley 0.1\u20130.2 mm. PHOTO: Sandra Kozak, EMBL Hamburg.<\/figcaption><\/figure>\n\n\n\n

Pin-pointed<\/h3>\n\n\n\n

Having solved the mystery of the bi-specificity, however, the story didn\u2019t end there. Rentmeister\u2019s team did a number of mutation studies, creating mutants of the enzyme to identify exactly which of the residues in the enzyme was responsible for the bi-specificity. \u201cWe pin-pointed it to three residues,\u201d she explains. \u201cBy changing these residues, we could create mono-specificity for Arginine or Tyrosine, which as far as we know is not found in nature.\u201d<\/p>\n\n\n\n

Reprogrammed NRPS enzymes could be used to produce novel peptides with interesting properties.<\/p><\/blockquote>\n\n\n\n

Looking at the structures of the two amino acids, Meijers wondered whether a so-called non-natural amino acid \u2013 4-azidophenylalanine \u2013 could fit the pocket and be activated by the enzyme. \u201cThis man-made amino acid is a sort of chemical chimera of Arginine and Tyrosine,\u201d he says. And, indeed, one of the mutant enzymes took up this non-natural amino acid. The results, published in Angewandte Chemie<\/em>, point to several promising future research directions. \u201cThat the NRPS enzyme could accept non-natural amino acids and potentially incorporate them into the poly-peptide chain, opens up a number of exciting possibilities,\u201d says Meijers. \u201cFor example, reprogrammed NRPS enzymes could be used to produce novel peptides with interesting properties.\u201d<\/p>\n\n\n\n

\u201cIt is also not really understood why these cyanobacteria produce toxic blooms in summer,\u201d adds Rentmeister. \u201cWe can now design an amino acid to include a traceable tag and map cellular pathways and processes.\u201d<\/p>\n\n\n\n

\"Left:
Left: Overall view of the binding domain of the non-ribosomal peptide synthetase, with Tyrosine in the binding pocket. Right: Overlay of Tyrosine (white) and Arginine (cyan) substrates, showing shape mimicry<\/figcaption><\/figure>\n\n\n\n

Worth it<\/h3>\n\n\n\n

Rentmeister explains that the experience with the SPC team at EMBL Hamburg proved indispensable. \u201cBi-specificity has not been observed in this group of enzymes before Guntram\u2019s work and now with the help of Rob\u2019s team we have shown how this is achieved and how we might use this for protein engineering and synthetic biology approaches. It took a while, but it was worth it!\u201d she concludes.<\/p>\n\n\n\n

\u201cAndrea is exactly the kind of person we want to support,\u201d says Meijers. \u201cAs a non-expert, she came to us with an interesting structural biological question, which we helped to answer \u2013 this was a really exciting project to be part of.\u201d Rentmeister is now keen to come back to EMBL Hamburg with more enzymes and has signed up to access the SPC facility via the latest transnational access project, BioStruct-X. \u201cI\u2019ll be back!\u201d she says with a smile.<\/p>\n","protected":false},"excerpt":{"rendered":"

A puzzling peculiarity resolved by Hamburg\u2019s Sample Preparation and Characterisation facility.<\/p>\n","protected":false},"author":18,"featured_media":4244,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[29,53,100,76,35],"embl_taxonomy":[],"class_list":["post-4234","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-crystallography","tag-hamburg","tag-meijers","tag-service","tag-structural-biology"],"acf":{"article_intro":"

When Andrea Rentmeister from the University of Muenster came across an enzyme with curious bi-specific properties, she was eager to find out more about its molecular 3D structure. As a chemist with no expertise in protein crystalisation she turned to the Sample Preparation and Characterisation (SPC) facility at EMBL Hamburg for help. What started out as a shot in the dark, resulted in a crystal structure \u2013 shedding light onto this peculiar feature.<\/p>\n","related_links":[{"link_description":"Sample Preparation and Characterisation (SPC) facility, EMBL Hamburg","link_url":"http:\/\/www.embl-hamburg.de\/services\/spc\/"},{"link_description":"EMBL beamlines at PETRA III (DESY Research Centre, Hamburg)","link_url":"http:\/\/www.embl-hamburg.de\/services\/mx\/index.html"},{"link_description":"Andrea Rentmeister, University of M\u00fcnster","link_url":"https:\/\/www.uni-muenster.de\/Cells-in-Motion\/people\/all\/rentmeister-a.php"},{"link_description":"University of Innsbruck, Research Institute for Limnology","link_url":"http:\/\/www.uibk.ac.at\/limno\/personnel\/kurmayer\/index.html.en"},{"link_description":"BioStruct-X \u2013 transnational access project","link_url":"http:\/\/www.biostruct-x.eu\/"}],"article_sources":[{"source_description":"

Kaljunen H\u00a0et al.\u00a0Angewandte Chemie,<\/em>\u00a011 June 2015.\u00a0<\/em>DOI:\u00a010.1002\/ange.201503275<\/p>\n","source_link_url":"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/anie.201503275\/abstract"}],"vf_locked":false,"featured":false,"color":"#007B53"},"embl_taxonomy_terms":[],"yoast_head":"\nThe curious case of the bi-specific enzyme | EMBL<\/title>\n<meta name=\"description\" content=\"Andrea Rentmeister turned to the Sample Preparation and Characterisation facility to help shed light on a cyanobacteria enzyme with bi-specific properties.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The curious case of the bi-specific enzyme | EMBL\" \/>\n<meta property=\"og:description\" content=\"Andrea Rentmeister turned to the Sample Preparation and Characterisation facility to help shed light on a cyanobacteria enzyme with bi-specific properties.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2015-06-18T08:25:52+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-11-29T15:52:58+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/06\/1506-spc-ib.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"620\" \/>\n\t<meta property=\"og:image:height\" content=\"425\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Rosemary Wilson\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@rawilson80\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Rosemary Wilson\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"6 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/\"},\"author\":{\"name\":\"Rosemary Wilson\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/bb5e57a6c6c5c3b33a6a40b2d4c96e40\"},\"headline\":\"The curious case of the bi-specific enzyme\",\"datePublished\":\"2015-06-18T08:25:52+00:00\",\"dateModified\":\"2024-11-29T15:52:58+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/\"},\"wordCount\":1222,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/06\/1506-spc-ib.jpg\",\"keywords\":[\"crystallography\",\"hamburg\",\"meijers\",\"service\",\"structural biology\"],\"articleSection\":[\"Science\",\"Science & Technology\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/\",\"url\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/\",\"name\":\"The curious case of the bi-specific enzyme | EMBL\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/06\/1506-spc-ib.jpg\",\"datePublished\":\"2015-06-18T08:25:52+00:00\",\"dateModified\":\"2024-11-29T15:52:58+00:00\",\"description\":\"Andrea Rentmeister turned to the Sample Preparation and Characterisation facility to help shed light on a cyanobacteria enzyme with bi-specific properties.\",\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/1506-enzyme\/#primaryimage\",\"url\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/06\/1506-spc-ib.jpg\",\"contentUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/06\/1506-spc-ib.jpg\",\"width\":620,\"height\":425,\"caption\":\"A large bloom of cyanobacteria on a lake in Central America. 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