1v0t
From Proteopedia
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| - | [[Image:1v0t.jpg|left|200px]] | + | [[Image:1v0t.jpg|left|200px]] |
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| - | '''PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE PRODUCT GLYCEROPHOSPHATE''' | + | {{Structure |
| + | |PDB= 1v0t |SIZE=350|CAPTION= <scene name='initialview01'>1v0t</scene>, resolution 1.53Å | ||
| + | |SITE= <scene name='pdbsite=CAT:Catalytic+Residues'>CAT</scene> | ||
| + | |LIGAND= <scene name='pdbligand=PO3:PHOSPHITE ION'>PO3</scene> | ||
| + | |ACTIVITY= [http://en.wikipedia.org/wiki/Phospholipase_D Phospholipase D], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.4 3.1.4.4] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE PRODUCT GLYCEROPHOSPHATE''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1V0T is a [ | + | 1V0T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V0T OCA]. |
==Reference== | ==Reference== | ||
| - | The reaction mechanism of phospholipase D from Streptomyces sp. strain PMF. Snapshots along the reaction pathway reveal a pentacoordinate reaction intermediate and an unexpected final product., Leiros I, McSweeney S, Hough E, J Mol Biol. 2004 Jun 11;339(4):805-20. PMID:[http:// | + | The reaction mechanism of phospholipase D from Streptomyces sp. strain PMF. Snapshots along the reaction pathway reveal a pentacoordinate reaction intermediate and an unexpected final product., Leiros I, McSweeney S, Hough E, J Mol Biol. 2004 Jun 11;339(4):805-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15165852 15165852] |
[[Category: Phospholipase D]] | [[Category: Phospholipase D]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: product soak]] | [[Category: product soak]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:39:26 2008'' |
Revision as of 12:39, 20 March 2008
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| , resolution 1.53Å | |||||||
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| Sites: | |||||||
| Ligands: | |||||||
| Activity: | Phospholipase D, with EC number 3.1.4.4 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE PRODUCT GLYCEROPHOSPHATE
Overview
Almost all enzyme-catalysed phosphohydrolytic or phosphoryl transfer reactions proceed through a five-coordinated phosphorus transition state. This is also true for the phospholipase D superfamily of enzymes, where the active site usually is made up of two identical sequence repeats of an HKD motif, positioned around an approximate 2-fold axis, where the histidine and lysine residues are essential for catalysis. An almost complete reaction pathway has been elucidated by a series of experiments where crystals of phospholipase D from Streptomyces sp. strain PMF (PLD(PMF)) were soaked for different times with (i) a soluble poor, short-chained phospholipid substrate and (ii) with a product. The various crystal structures were determined to a resolution of 1.35-1.75 A for the different time-steps. Both substrate and product-structures were determined in order to identify the different reaction states and to examine if the reaction actually terminated on formation of phosphatidic acid (the true product of phospholipase D action) or could proceed even further. The results presented support the theory that the phospholipase D superfamily shares a common reaction mechanism, although different family members have very different substrate preferences and perform different catalytic reactions. Results also show that the reaction proceeds via a phosphohistidine intermediate and provide unambiguous identification of a catalytic water molecule, ideally positioned for apical attack on the phosphorus and consistent with an associative in-line phosphoryl transfer reaction. In one of the experiments an apparent five-coordinate phosphorus transition state is observed.
About this Structure
1V0T is a Single protein structure of sequence from Streptomyces sp.. Full crystallographic information is available from OCA.
Reference
The reaction mechanism of phospholipase D from Streptomyces sp. strain PMF. Snapshots along the reaction pathway reveal a pentacoordinate reaction intermediate and an unexpected final product., Leiros I, McSweeney S, Hough E, J Mol Biol. 2004 Jun 11;339(4):805-20. PMID:15165852
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