1ycl

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[[Image:1ycl.gif|left|200px]]<br /><applet load="1ycl" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1ycl.gif|left|200px]]
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caption="1ycl, resolution 1.80&Aring;" />
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'''Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate'''<br />
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{{Structure
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|PDB= 1ycl |SIZE=350|CAPTION= <scene name='initialview01'>1ycl</scene>, resolution 1.80&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=KRI:(S)-2-AMINO-4-[(2S,3R)-2,3,5-TRIHYDROXY-4-OXO-PENTYL]MERCAPTO-BUTYRIC ACID'>KRI</scene>
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|ACTIVITY=
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|GENE= luxS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
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}}
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'''Crystal Structure of B. subtilis LuxS in Complex with a Catalytic 2-Ketone Intermediate'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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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].
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1YCL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCL OCA].
==Reference==
==Reference==
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15751951 15751951]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/15751951 15751951]
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Single protein]]
[[Category: Single protein]]
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[[Category: quorum sensing]]
[[Category: quorum sensing]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:04:00 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:21:08 2008''

Revision as of 13:21, 20 March 2008

Image:1ycl.gif


PDB ID 1ycl

Drag the structure with the mouse to rotate
, resolution 1.80Å
Ligands: , and
Gene: luxS (Bacillus subtilis)
Coordinates: save as pdb, mmCIF, xml



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. 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

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