1q5p
From Proteopedia
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|PDB= 1q5p |SIZE=350|CAPTION= <scene name='initialview01'>1q5p</scene>, resolution 1.6Å | |PDB= 1q5p |SIZE=350|CAPTION= <scene name='initialview01'>1q5p</scene>, resolution 1.6Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SEB:O-BENZYLSULFONYL-SERINE'>SEB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q5p OCA], [http://www.ebi.ac.uk/pdbsum/1q5p PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q5p RCSB]</span> | ||
}} | }} | ||
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[[Category: Knapp, M.]] | [[Category: Knapp, M.]] | ||
[[Category: Murray, C J.]] | [[Category: Murray, C J.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: SO4]] | ||
[[Category: altered flexibility]] | [[Category: altered flexibility]] | ||
[[Category: serine protease]] | [[Category: serine protease]] | ||
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[[Category: subtilisin]] | [[Category: subtilisin]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:09:08 2008'' |
Revision as of 20:09, 30 March 2008
| |||||||
| , resolution 1.6Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Subtilisin, with EC number 3.4.21.62 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
S156E/S166D variant of Bacillus lentus subtilisin
Overview
The properties of the transition state for serine protease-catalyzed hydrolysis of an amide bond were determined for a series of subtilisin variants from Bacillus lentus. There is no significant change in the structure of the enzyme upon introduction of charged mutations S156E/S166D, suggesting that changes in catalytic activity reflect global properties of the enzyme. The effect of charged mutations on the pK(a) of the active site histidine-64 N(epsilon)(2)-H was correlated with changes in the second-order rate constant k(cat)/K(m) for hydrolysis of tetrapeptide anilides at low ionic strength with a Bronsted slope alpha = 1.1. The solvent isotope effect (D)2(O)(k(cat)/K(m))(1) = 1.4 +/- 0.2. These results are consistent with a rate-limiting breakdown of the tetrahedral intermediate in the acylation step with hydrogen bond stabilization of the departing amine leaving group. There is an increase in the ratio of hydrolysis of succinyl-Ala-Ala-Pro-Phe-anilides for p-nitroaniline versus aniline leaving groups with variants with more basic active site histidines that can be described by the interaction coefficient p(xy) = delta beta(lg)/delta pK(a) (H64) = 0.15. This is attributed to increased hydrogen bonding of the active site imidazolium N-H to the more basic amine leaving group as well as electrostatic destabilization of the transition state. A qualitative characterization of the transition state is presented in terms of a reaction coordinate diagram that is defined by the structure-reactivity parameters.
About this Structure
1Q5P is a Single protein structure of sequence from Bacillus lentus. Full crystallographic information is available from OCA.
Reference
Do enzymes change the nature of transition states? Mapping the transition state for general acid-base catalysis of a serine protease., Bott RR, Chan G, Domingo B, Ganshaw G, Hsia CY, Knapp M, Murray CJ, Biochemistry. 2003 Sep 16;42(36):10545-53. PMID:12962477
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