2v2a: Difference between revisions

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-{{Seed}}
-[[Image:2v2a.png|left|200px]]
-<!--
+==L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A- K248G-R253A-E254A)==
-The line below this paragraph, containing "STRUCTURE_2v2a", creates the "Structure Box" on the page.
+<StructureSection load='2v2a' size='340' side='right'caption='[[2v2a]], [[Resolution|resolution]] 1.75&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'>[[2v2a]] is a 1 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=2V2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V2A 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]] 1.75&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2v2a|  PDB=2v2a  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2v2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v2a OCA], [https://pdbe.org/2v2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v2a RCSB], [https://www.ebi.ac.uk/pdbsum/2v2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v2a ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RHAD_ECOLI RHAD_ECOLI] Catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde.[HAMAP-Rule:MF_00770]
+== 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/v2/2v2a_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2v2a ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The enzyme l-rhamnulose-1-phosphate aldolase from Escherichia coli participates in the degradation pathway of l-rhamnose, a ubiquitous deoxy-hexose. It is a homotetramer of the rare C4-symmetric type with N-terminal domains protruding like antennas from the main body. A mobility analysis of the enzyme gave rise to the hypothesis that an anisotropic thermal antenna motion may support the catalysis (Kroemer et al., Biochemistry 42, 10560, 2003). We checked this hypothesis by generating four single mutants and one disulfide bridge that were designed to reduce the mobility of the antenna domain without disturbing the chain-fold or the active center. The catalytic rates of the mutants revealed activity reductions that correlated well with the expected antenna fixation. Among these mutants, K15W was crystallized, structurally elucidated, and used as a guide for modeling the others. The structure confirmed the design because the mutation introduced a tight nonpolar contact to a neighboring subunit that fixed the antenna but did not affect the main chain. The fixation was confirmed by a comparison of the anisotropic B-factors describing the mobility of the domains. It turned out that the distinctly anisotropic mobility of the wild-type antenna domain has become isotropic in K15W, in agreement with the design. We suggest that, like K15W, the other mutations also followed the design, validating the correlation between antenna mobility and activity. This correlation suggests that the domain mobility facilitates the reaction.
-===L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248G-R253A-E254A)===
+Antenna domain mobility and enzymatic reaction of L-rhamnulose-1-phosphate aldolase.,Grueninger D, Schulz GE Biochemistry. 2008 Jan 15;47(2):607-14. Epub 2007 Dec 18. PMID:18085797<ref>PMID:18085797</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2v2a" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18085797}}, adds the Publication Abstract to the page
+*[[Aldolase 3D structures|Aldolase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18085797 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18085797}}
+__TOC__
+</StructureSection>
-==About this Structure==
-V2A is a 1 chain 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=2V2A OCA].
-==Reference==
-<ref group="xtra">PMID:18085797</ref><ref group="xtra">PMID:12962479</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Rhamnulose-1-phosphate aldolase]]
+[[Category: Large Structures]]
-[[Category: Grueninger, D.]]
+[[Category: Grueninger D]]
-[[Category: Schulz, G E.]]
+[[Category: Schulz GE]]
-[[Category: 2-ketose degradation]]
-[[Category: Aldolase]]
-[[Category: Bacterial l-rhamnose metabolism]]
-[[Category: Class ii]]
-[[Category: Cleavage of l-rhamnulose-1-phosphate to dihydroxyacetone phosphate]]
-[[Category: Domain motion for mechanical support of catalysis]]
-[[Category: Lyase]]
-[[Category: Metal-binding]]
-[[Category: Protein engineering]]
-[[Category: Protein-protein interface]]
-[[Category: Rare sugar]]
-[[Category: Rhamnose metabolism]]
-[[Category: Surface mutation]]
-[[Category: Zinc]]
-[[Category: Zinc enzyme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:15:16 2009''