1jcl

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[[Image:1jcl.gif|left|200px]]
 
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{{Structure
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==OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION==
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|PDB= 1jcl |SIZE=350|CAPTION= <scene name='initialview01'>1jcl</scene>, resolution 1.05&Aring;
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<StructureSection load='1jcl' size='340' side='right'caption='[[1jcl]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene>
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<table><tr><td colspan='2'>[[1jcl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JCL FirstGlance]. <br>
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|ACTIVITY= [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]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPD:1-HYDROXY-PENTANE-3,4-DIOL-5-PHOSPHATE'>HPD</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jcl OCA], [https://pdbe.org/1jcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jcl RCSB], [https://www.ebi.ac.uk/pdbsum/1jcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jcl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DEOC_ECOLI DEOC_ECOLI] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.[HAMAP-Rule:MF_00592]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jcl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jcl ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION'''
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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<ref>PMID:11598300</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1jcl" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[Aldolase 3D structures|Aldolase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1JCL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JCL OCA].
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__TOC__
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</StructureSection>
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/11598300 11598300]
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[[Category: Deoxyribose-phosphate aldolase]]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: DeSantis, G.]]
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[[Category: DeSantis G]]
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[[Category: Heine, A.]]
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[[Category: Heine A]]
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[[Category: Luz, J G.]]
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[[Category: Luz JG]]
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[[Category: Mitchell, M.]]
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[[Category: Mitchell M]]
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[[Category: Wilson, I A.]]
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[[Category: Wilson IA]]
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[[Category: Wong, C H.]]
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[[Category: Wong C-H]]
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[[Category: HPD]]
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[[Category: alpha-beta tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:01:34 2008''
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Current revision

OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION

PDB ID 1jcl

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