1ycl
From Proteopedia
(New page: 200px<br /><applet load="1ycl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ycl, resolution 1.80Å" /> '''Crystal Structure of...) |
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| - | [[Image:1ycl.gif|left|200px]]<br /><applet load="1ycl" size=" | + | [[Image:1ycl.gif|left|200px]]<br /><applet load="1ycl" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ycl, resolution 1.80Å" /> | caption="1ycl, resolution 1.80Å" /> | ||
'''Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate'''<br /> | '''Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate'''<br /> | ||
==Overview== | ==Overview== | ||
| - | S-Ribosylhomocysteinase (LuxS) is an Fe(2+)-dependent metalloenzyme that | + | S-Ribosylhomocysteinase (LuxS) is an Fe(2+)-dependent metalloenzyme that catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum-sensing molecule. The proposed mechanism involves an initial metal-catalyzed aldose-ketose isomerization reaction, which results in the migration of the ribose carbonyl group from its C1 to C2 position and the formation of a 2-ketone intermediate. A repetition of the isomerization reaction shifts the carbonyl group to the C3 position. Subsequent beta-elimination reaction at the C4 and C5 positions completes the catalytic cycle. In this work, a catalytically inactive mutant (C84A) of Co(2+)-substituted Bacillus subtilis LuxS was cocrystallized with the 2-ketone intermediate and the structure was determined to 1.8 A resolution. The structure reveals that the C2 carbonyl oxygen is directly coordinated with the metal ion, providing strong support for the proposed Lewis acid function of the metal ion during catalysis. Cys-84 and Glu-57 are optimally positioned to act as general acids/bases during the isomerization and elimination reactions. In addition, Ser-6, His-11, and Arg-39 are involved in substrate/ intermediate binding through hydrogen bonding interactions. The above conclusions are further confirmed by site-directed mutagenesis and visible absorption spectroscopic studies. |
==About this Structure== | ==About this Structure== | ||
| - | 1YCL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with CO, SO4 and KRI as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1YCL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=CO:'>CO</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=KRI:'>KRI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCL OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Bell, C | + | [[Category: Bell, C E.]] |
[[Category: Hu, X.]] | [[Category: Hu, X.]] | ||
[[Category: Pei, D.]] | [[Category: Pei, D.]] | ||
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[[Category: quorum sensing]] | [[Category: quorum sensing]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:04:00 2008'' |
Revision as of 14:04, 21 February 2008
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Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate
Overview
S-Ribosylhomocysteinase (LuxS) is an Fe(2+)-dependent metalloenzyme that catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine (Hcys) and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum-sensing molecule. The proposed mechanism involves an initial metal-catalyzed aldose-ketose isomerization reaction, which results in the migration of the ribose carbonyl group from its C1 to C2 position and the formation of a 2-ketone intermediate. A repetition of the isomerization reaction shifts the carbonyl group to the C3 position. Subsequent beta-elimination reaction at the C4 and C5 positions completes the catalytic cycle. In this work, a catalytically inactive mutant (C84A) of Co(2+)-substituted Bacillus subtilis LuxS was cocrystallized with the 2-ketone intermediate and the structure was determined to 1.8 A resolution. The structure reveals that the C2 carbonyl oxygen is directly coordinated with the metal ion, providing strong support for the proposed Lewis acid function of the metal ion during catalysis. Cys-84 and Glu-57 are optimally positioned to act as general acids/bases during the isomerization and elimination reactions. In addition, Ser-6, His-11, and Arg-39 are involved in substrate/ intermediate binding through hydrogen bonding interactions. The above conclusions are further confirmed by site-directed mutagenesis and visible absorption spectroscopic studies.
About this Structure
1YCL is a Single protein structure of sequence from Bacillus subtilis with , and as ligands. Full crystallographic information is available from OCA.
Reference
Crystal structure of S-ribosylhomocysteinase (LuxS) in complex with a catalytic 2-ketone intermediate., Rajan R, Zhu J, Hu X, Pei D, Bell CE, Biochemistry. 2005 Mar 15;44(10):3745-53. PMID:15751951
Page seeded by OCA on Thu Feb 21 16:04:00 2008
Categories: Bacillus subtilis | Single protein | Bell, C E. | Hu, X. | Pei, D. | Rajan, R. | Zhu, J. | CO | KRI | SO4 | Metalloenzyme | Quorum sensing
