3b5v
From Proteopedia
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[[Image:3b5v.jpg|left|200px]] | [[Image:3b5v.jpg|left|200px]] | ||
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| - | | | + | {{STRUCTURE_3b5v| PDB=3b5v | SCENE= }} |
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'''Crystal Structure of a Novel Engineered Retroaldolase: RA-22''' | '''Crystal Structure of a Novel Engineered Retroaldolase: RA-22''' | ||
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| + | ==Overview== | ||
| + | The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model. | ||
==About this Structure== | ==About this Structure== | ||
3B5V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B5V OCA]. | 3B5V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B5V OCA]. | ||
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| + | ==Reference== | ||
| + | De novo computational design of retro-aldol enzymes., Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF 3rd, Hilvert D, Houk KN, Stoddard BL, Baker D, Science. 2008 Mar 7;319(5868):1387-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18323453 18323453] | ||
[[Category: Indole-3-glycerol-phosphate synthase]] | [[Category: Indole-3-glycerol-phosphate synthase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: Doyle, L A.]] | [[Category: Doyle, L A.]] | ||
[[Category: Stoddard, B L.]] | [[Category: Stoddard, B L.]] | ||
| - | [[Category: | + | [[Category: Engineered computationally designed]] |
| - | [[Category: | + | [[Category: Lyase]] |
| - | [[Category: | + | [[Category: Retroaldolase]] |
| - | [[Category: | + | [[Category: Tim barrel]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:25:28 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 17:25, 4 May 2008
Crystal Structure of a Novel Engineered Retroaldolase: RA-22
Overview
The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retro-aldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.
About this Structure
3B5V is a Single protein structure of sequence from Sulfolobus solfataricus. Full crystallographic information is available from OCA.
Reference
De novo computational design of retro-aldol enzymes., Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF 3rd, Hilvert D, Houk KN, Stoddard BL, Baker D, Science. 2008 Mar 7;319(5868):1387-91. PMID:18323453 Page seeded by OCA on Sun May 4 20:25:28 2008
