1v0w
From Proteopedia
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|PDB= 1v0w |SIZE=350|CAPTION= <scene name='initialview01'>1v0w</scene>, resolution 1.35Å | |PDB= 1v0w |SIZE=350|CAPTION= <scene name='initialview01'>1v0w</scene>, resolution 1.35Å | ||
|SITE= <scene name='pdbsite=CAT:Po3+Binding+Site+For+Chain+A'>CAT</scene> | |SITE= <scene name='pdbsite=CAT:Po3+Binding+Site+For+Chain+A'>CAT</scene> | ||
| - | |LIGAND= <scene name='pdbligand=PO3:PHOSPHITE ION'>PO3</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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1v0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v0w OCA], [http://www.ebi.ac.uk/pdbsum/1v0w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1v0w RCSB]</span> | ||
}} | }} | ||
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[[Category: Leiros, I.]] | [[Category: Leiros, I.]] | ||
[[Category: Mcsweeney, S.]] | [[Category: Mcsweeney, S.]] | ||
| - | [[Category: PO3]] | ||
[[Category: dibutyrylphosphatidylcholine]] | [[Category: dibutyrylphosphatidylcholine]] | ||
[[Category: dic4pc]] | [[Category: dic4pc]] | ||
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[[Category: substrate soak]] | [[Category: substrate soak]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:18:03 2008'' |
Revision as of 21:18, 30 March 2008
| |||||||
| , resolution 1.35Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | |||||||
| Activity: | Phospholipase D, with EC number 3.1.4.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE.
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
1V0W 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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