1j1y: Difference between revisions
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'''Crystal Structure of PaaI from Thermus thermophilus HB8''' | {{Structure | ||
|PDB= 1j1y |SIZE=350|CAPTION= <scene name='initialview01'>1j1y</scene>, resolution 1.7Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Crystal Structure of PaaI from Thermus thermophilus HB8''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1J1Y is a [ | 1J1Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J1Y OCA]. | ||
==Reference== | ==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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/16061252 16061252] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
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[[Category: riken structural genomics/proteomics initiative]] | [[Category: riken structural genomics/proteomics initiative]] | ||
[[Category: rsgi]] | [[Category: rsgi]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
[[Category: thioesterase]] | [[Category: thioesterase]] | ||
''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 11:57:51 2008'' | ||
Revision as of 09:58, 20 March 2008
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| 1j1y, resolution 1.7Å | |||||||||||||
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| Ligands: | CL and MG | ||||||||||||
| 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
Page seeded by OCA on Thu Mar 20 11:57:51 2008
Proteopedia Page Contributors and Editors (what is this?)
- Pages with broken file links
- Single protein
- Thermus thermophilus
- Kunishima, N.
- Kuramitsu, S.
- Miyano, M.
- RSGI, RIKEN Structural Genomics/Proteomics Initiative.
- Sugahara, M.
- Yokoyama, S.
- CL
- MG
- Hot dog fold
- Phenylacetic acid degradation
- Riken structural genomics/proteomics initiative
- Rsgi
- Structural genomic
- Thioesterase
