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2vwt

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{{Seed}}
 
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[[Image:2vwt.png|left|200px]]
 
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==Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex==
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The line below this paragraph, containing "STRUCTURE_2vwt", creates the "Structure Box" on the page.
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<StructureSection load='2vwt' size='340' side='right'caption='[[2vwt]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2vwt]] 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=2VWT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VWT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.93&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
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{{STRUCTURE_2vwt| PDB=2vwt | SCENE= }}
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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=2vwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwt OCA], [https://pdbe.org/2vwt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vwt RCSB], [https://www.ebi.ac.uk/pdbsum/2vwt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vwt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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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/vw/2vwt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2vwt 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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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.
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===CRYSTAL STRUCTURE OF YFAU, A METAL ION DEPENDENT CLASS II ALDOLASE FROM ESCHERICHIA COLI K12 - MG-PYRUVATE PRODUCT COMPLEX===
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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>
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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 2vwt" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18754683}}, adds the Publication Abstract to the page
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*[[Aldolase 3D structures|Aldolase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18754683 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18754683}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli K-12]]
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2VWT 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=2VWT OCA].
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[[Category: Large Structures]]
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[[Category: Bugg TDH]]
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==Reference==
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[[Category: Fulop V]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/18754683 18754683]
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[[Category: Gerlt JA]]
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[[Category: 2-dehydro-3-deoxyglucarate aldolase]]
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[[Category: Rakus JF]]
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[[Category: Escherichia coli]]
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[[Category: Rea D]]
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[[Category: Single protein]]
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[[Category: Roper DI]]
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[[Category: Bugg, T D.H.]]
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[[Category: Fulop, V.]]
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[[Category: Gerlt, J A.]]
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[[Category: Rakus, J F.]]
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[[Category: Rea, D.]]
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[[Category: Roper, D I.]]
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[[Category: 2-keto-3-deoxy sugar aldolase]]
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[[Category: Class ii aldolase]]
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[[Category: Degradation of homoprotocatechuate]]
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[[Category: Escherichia coli k-12 protein yfau]]
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[[Category: Lyase]]
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[[Category: Pyruvate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 1 20:38:01 2008''
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Current revision

Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex

PDB ID 2vwt

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