1e6a: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 5: | Line 5: | ||
==Overview== | ==Overview== | ||
The wealth of kinetic and structural information makes inorganic, pyrophosphatases (PPases) a good model system to study the details of, enzymatic phosphoryl transfer. The enzyme accelerates metal-complexed, phosphoryl transfer 10(10)-fold: but how? Our structures of the yeast, PPase product complex at 1.15 A and fluoride-inhibited complex at 1.9 A, visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound. These span the steps, around chemical catalysis and provide strong evidence that a water, molecule (O(nu)) directly attacks PPi with a pK(a) vastly lowered by, coordination to two metal ions and D117. They also suggest that a, low-barrier hydrogen bond (LBHB) forms between D117 and O(nu), in part, because of steric crowding ... | The wealth of kinetic and structural information makes inorganic, pyrophosphatases (PPases) a good model system to study the details of, enzymatic phosphoryl transfer. The enzyme accelerates metal-complexed, phosphoryl transfer 10(10)-fold: but how? Our structures of the yeast, PPase product complex at 1.15 A and fluoride-inhibited complex at 1.9 A, visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound. These span the steps, around chemical catalysis and provide strong evidence that a water, molecule (O(nu)) directly attacks PPi with a pK(a) vastly lowered by, coordination to two metal ions and D117. They also suggest that a, low-barrier hydrogen bond (LBHB) forms between D117 and O(nu), in part, because of steric crowding by W100 and N116. Direct visualization of the, double bonds on the phosphates appears possible. The flexible side chains, at the top of the active site absorb the motion involved in the reaction, which may help accelerate catalysis. Relaxation of the product allows a, new nucleophile to be generated and creates symmetry in the elementary, catalytic steps on the enzyme. We are thus moving closer to understanding, phosphoryl transfer in PPases at the quantum mechanical level. Ultra-high, resolution structures can thus tease out overlapping complexes and so are, as relevant to discussion of enzyme mechanism as structures produced by, time-resolved crystallography. | ||
==About this Structure== | ==About this Structure== | ||
1E6A is a | 1E6A is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MN, F, NA, PO4, POP and POP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Structure known Active Sites: POA and POB. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1E6A OCA]. | ||
==Reference== | ==Reference== | ||
| Line 31: | Line 31: | ||
[[Category: phosphoryl transfer]] | [[Category: phosphoryl transfer]] | ||
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 14:08:10 2007'' | ||
