1j1y: Difference between revisions
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|PDB= 1j1y |SIZE=350|CAPTION= <scene name='initialview01'>1j1y</scene>, resolution 1.7Å | |PDB= 1j1y |SIZE=350|CAPTION= <scene name='initialview01'>1j1y</scene>, resolution 1.7Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j1y OCA], [http://www.ebi.ac.uk/pdbsum/1j1y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j1y RCSB]</span> | |||
}} | }} | ||
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[[Category: Sugahara, M.]] | [[Category: Sugahara, M.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
[[Category: hot dog fold]] | [[Category: hot dog fold]] | ||
[[Category: phenylacetic acid degradation]] | [[Category: phenylacetic acid degradation]] | ||
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[[Category: thioesterase]] | [[Category: thioesterase]] | ||
''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 21:27:44 2008'' | ||
Revision as of 18:27, 30 March 2008
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| 1j1y, resolution 1.7Å | |||||||||||||
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| Ligands: | CL, MG | ||||||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Crystal Structure of PaaI from Thermus thermophilus HB8
Overview
Hot dog fold proteins sharing the characteristic "hot dog" fold are known to involve certain coenzyme A binding enzymes with various oligomeric states. In order to elucidate the oligomerization-function relationship of the hot dog fold proteins, crystal structures of the phenylacetate degradation protein PaaI from Thermus thermophilus HB8 (TtPaaI), a tetrameric acyl-CoA thioesterase with the hot dog fold, have been determined and compared with those of other family members. In the liganded crystal forms with coenzyme A derivatives, only two of four intersubunit catalytic pockets of the TtPaaI tetramer are occupied by the ligands. A detailed structural comparison between several liganded and unliganded forms reveals that a subtle rigid-body rearrangement of subunits within 2 degrees upon binding of the first two ligand molecules can induce a strict negative cooperativity to prevent further binding at the remaining two pockets, indicating that the so-called "half-of-the-sites reactivity" of oligomeric enzymes is visualized for the first time. Considering kinetic and mutational analyses together, a possible reaction mechanism of TtPaaI is proposed; one tetramer binds only two acyl-CoA molecules with a novel asymmetric induced-fit mechanism and carries out the hydrolysis according to a base-catalyzed reaction through activation of a water molecule by Asp48. From a structural comparison with other family members, it is concluded that a subgroup of the hot dog fold protein family, referred to as "asymmetric hot dog thioesterases" including medium chain acyl-CoA thioesterase II from Escherichia coli and human thioesterase III, might share the same oligomerization mode and the asymmetric induced-fit mechanism as observed in TtPaaI.
About this Structure
1J1Y is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.
Reference
A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI., Kunishima N, Asada Y, Sugahara M, Ishijima J, Nodake Y, Sugahara M, Miyano M, Kuramitsu S, Yokoyama S, Sugahara M, J Mol Biol. 2005 Sep 9;352(1):212-28. PMID:16061252
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