1wm6
From Proteopedia
(New page: 200px<br /><applet load="1wm6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wm6, resolution 2.40Å" /> '''Crystal structure of...) |
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| - | [[Image:1wm6.gif|left|200px]]<br /><applet load="1wm6" size=" | + | [[Image:1wm6.gif|left|200px]]<br /><applet load="1wm6" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wm6, resolution 2.40Å" /> | caption="1wm6, resolution 2.40Å" /> | ||
'''Crystal structure of TT0310 protein from Thermus thermophilus HB8'''<br /> | '''Crystal structure of TT0310 protein from Thermus thermophilus HB8'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Hot dog fold proteins sharing the characteristic "hot dog" fold are known | + | 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== | ==About this Structure== | ||
| - | 1WM6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with CL as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1WM6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WM6 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Kunishima, N.]] | [[Category: Kunishima, N.]] | ||
[[Category: Miyano, M.]] | [[Category: Miyano, M.]] | ||
| - | [[Category: RSGI, RIKEN | + | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] |
[[Category: Sugahara, M.]] | [[Category: Sugahara, M.]] | ||
[[Category: CL]] | [[Category: CL]] | ||
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[[Category: thioesterase]] | [[Category: thioesterase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:45:51 2008'' |
Revision as of 13:45, 21 February 2008
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Crystal structure of TT0310 protein 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
1WM6 is a Single protein structure of sequence from Thermus thermophilus with as ligand. 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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