2vws: Difference between revisions

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-[[Image:2vws.png|left|200px]]
-<!--
+==Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12==
-The line below this paragraph, containing "STRUCTURE_2vws", creates the "Structure Box" on the page.
+<StructureSection load='2vws' size='340' side='right'caption='[[2vws]], [[Resolution|resolution]] 1.39&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'>[[2vws]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VWS 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]] 1.39&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2vws|  PDB=2vws  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vws OCA], [https://pdbe.org/2vws PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vws RCSB], [https://www.ebi.ac.uk/pdbsum/2vws PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vws ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RHMA_ECOLI RHMA_ECOLI] Catalyzes the reversible retro-aldol cleavage of 2-keto-3-deoxy-L-rhamnonate (KDR) to pyruvate and lactaldehyde. 2-keto-3-deoxy-L-mannonate, 2-keto-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) are also reasonably good substrates, although 2-keto-3-deoxy-L-rhamnonate is likely to be the physiological substrate.<ref>PMID:18754683</ref> <ref>PMID:18754693</ref>
+== 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/vw/2vws_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=2vws ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+One of the major challenges in the postgenomic era is the functional assignment of proteins using sequence- and structure-based predictive methods coupled with experimental validation. We have used these approaches to investigate the structure and function of the Escherichia coli K-12 protein YfaU, annotated as a putative 4-hydroxy-2-ketoheptane-1,7-dioate aldolase (HpcH) in the sequence databases. HpcH is the final enzyme in the degradation pathway of the aromatic compound homoprotocatechuate. We have determined the crystal structure of apo-YfaU and the Mg (2+)-pyruvate product complex. Despite greater sequence and structural similarity to HpcH, genomic context suggests YfaU is instead a 2-keto-3-deoxy sugar aldolase like the homologous 2-dehydro-3-deoxygalactarate aldolase (DDGA). Enzyme kinetic measurements show activity with the probable physiological substrate 2-keto-3-deoxy- l-rhamnonate, supporting the functional assignment, as well as the structurally similar 2-keto-3-deoxy- l-mannonate and 2-keto-3-deoxy- l-lyxonate (see accompanying paper: Rakus, J. F., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Hubbard, B. K., Delli, J. D., Babbitt, P. C., Almo, S. C., and Gerlt, J. A. (2008) Biochemistry 47, XXXXX-XXXXX). YfaU has similar activity toward the HpcH substrate 4-hydroxy-2-ketoheptane-1,7-dioate and synthetic substrates 4-hydroxy-2-ketopentanoic acid and 4-hydroxy-2-ketohexanoic acid. This indicates a relaxed substrate specificity that complicates the functional assignment of members of this enzyme superfamily. Crystal structures suggest these enzymes use an Asp-His intersubunit dyad to activate a metal-bound water or hydroxide for proton transfer during catalysis.
-===CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12===
+Crystal Structure and Functional Assignment of YfaU, a Metal Ion Dependent Class II Aldolase from Escherichia coli K12.,Rea D, Hovington R, Rakus JF, Gerlt JA, Fulop V, Bugg TD, Roper DI Biochemistry. 2008 Aug 29. PMID:18754683<ref>PMID:18754683</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18754683}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vws" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18754683 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_18754683}}
-==About this Structure==
-[[2vws]] is a 3 chain structure of [[Aldolase]] with 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=2VWS OCA].
 ==See Also==
-*[[Aldolase]]
+*[[Aldolase 3D structures|Aldolase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018754683</ref><references group="xtra"/>
+__TOC__
-[[Category: 2-dehydro-3-deoxyglucarate aldolase]]
+</StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Bugg, T D.H.]]
+[[Category: Large Structures]]
-[[Category: Fulop, V.]]
+[[Category: Bugg TDH]]
-[[Category: Gerlt, J A.]]
+[[Category: Fulop V]]
-[[Category: Rakus, J F.]]
+[[Category: Gerlt JA]]
-[[Category: Rea, D.]]
+[[Category: Rakus JF]]
-[[Category: Roper, D I.]]
+[[Category: Rea D]]
-[[Category: 2-keto-3-deoxy sugar aldolase]]
+[[Category: Roper DI]]
-[[Category: Class ii aldolase]]
-[[Category: Degradation of homoprotocatechuate]]
-[[Category: Escherichia coli k-12 protein yfau]]
-[[Category: Lyase]]