1jcl: Difference between revisions

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{{Seed}}
[[Image:1jcl.png|left|200px]]


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==OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION==
The line below this paragraph, containing "STRUCTURE_1jcl", creates the "Structure Box" on the page.
<StructureSection load='1jcl' size='340' side='right'caption='[[1jcl]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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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<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>
{{STRUCTURE_1jcl|  PDB=1jcl  |  SCENE=  }}
<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>
</table>
== Function ==
[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]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jc/1jcl_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION===
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1jcl" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_11598300}}, adds the Publication Abstract to the page
*[[Aldolase 3D structures|Aldolase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 11598300 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_11598300}}
__TOC__
 
</StructureSection>
==About this Structure==
1JCL is a 2 chains structure of sequences 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].
 
==Reference==
<ref group="xtra">PMID:11598300</ref><references group="xtra"/>
[[Category: Deoxyribose-phosphate aldolase]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: DeSantis, G.]]
[[Category: Large Structures]]
[[Category: Heine, A.]]
[[Category: DeSantis G]]
[[Category: Luz, J G.]]
[[Category: Heine A]]
[[Category: Mitchell, M.]]
[[Category: Luz JG]]
[[Category: Wilson, I A.]]
[[Category: Mitchell M]]
[[Category: Wong, C H.]]
[[Category: Wilson IA]]
[[Category: Alpha-beta tim barrel]]
[[Category: Wong C-H]]
 
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Retrieved from "https://proteopedia.org/1jcl"