1jcl: Difference between revisions

Revision as of 14:21, 21 February 2008

OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION

OverviewOverview

In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.

About this StructureAbout this Structure

1JCL is a Single protein structure of sequence from Escherichia coli with as ligand. Active as Deoxyribose-phosphate aldolase, with EC number 4.1.2.4 Full crystallographic information is available from OCA.

ReferenceReference

Observation of covalent intermediates in an enzyme mechanism at atomic resolution., Heine A, DeSantis G, Luz JG, Mitchell M, Wong CH, Wilson IA, Science. 2001 Oct 12;294(5541):369-74. PMID:11598300

Page seeded by OCA on Thu Feb 21 13:21:06 2008

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OCA

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-[[Image:1jcl.gif|left|200px]]<br /><applet load="1jcl" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1jcl.gif|left|200px]]<br /><applet load="1jcl" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1jcl, resolution 1.05&Aring;" />
 '''OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION'''<br />
 ==Overview==
-In classical enzymology, intermediates and transition states in a, catalytic mechanism are usually inferred from a series of biochemical, experiments. Here, we derive an enzyme mechanism from true, atomic-resolution x-ray structures of reaction intermediates. Two, ultra-high resolution structures of wild-type and mutant, d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and, 1.10 angstroms unambiguously identify the postulated covalent, carbinolamine and Schiff base intermediates in the aldolase mechanism. In, combination with site-directed mutagenesis and (1)H nuclear magnetic, resonance, we can now propose how the heretofore elusive C-2 proton, abstraction step and the overall stereochemical course are accomplished. A, proton relay system appears to activate a conserved active-site water that, functions as the critical mediator for proton transfer.
+In classical enzymology, intermediates and transition states in a catalytic mechanism are usually inferred from a series of biochemical experiments. Here, we derive an enzyme mechanism from true atomic-resolution x-ray structures of reaction intermediates. Two ultra-high resolution structures of wild-type and mutant d-2-deoxyribose-5-phosphate (DRP) aldolase complexes with DRP at 1.05 and 1.10 angstroms unambiguously identify the postulated covalent carbinolamine and Schiff base intermediates in the aldolase mechanism. In combination with site-directed mutagenesis and (1)H nuclear magnetic resonance, we can now propose how the heretofore elusive C-2 proton abstraction step and the overall stereochemical course are accomplished. A proton relay system appears to activate a conserved active-site water that functions as the critical mediator for proton transfer.
 ==About this Structure==
-JCL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with HPD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1JCL OCA].
+JCL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=HPD:'>HPD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCL OCA].
 ==Reference==
@@ Line 16: / Line 16: @@
 [[Category: DeSantis, G.]]
 [[Category: Heine, A.]]
-[[Category: Luz, J.G.]]
+[[Category: Luz, J G.]]
 [[Category: Mitchell, M.]]
-[[Category: Wilson, I.A.]]
+[[Category: Wilson, I A.]]
-[[Category: Wong, C.H.]]
+[[Category: Wong, C H.]]
 [[Category: HPD]]
 [[Category: alpha-beta tim barrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:06:40 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:21:06 2008''