2vwt: Difference between revisions
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< | ==Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex== | ||
<StructureSection load='2vwt' size='340' side='right'caption='[[2vwt]], [[Resolution|resolution]] 1.93Å' scene=''> | |||
You may | == Structural highlights == | ||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> | ||
<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> | |||
</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/2vwt_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=2vwt 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 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2vwt" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Aldolase 3D structures|Aldolase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Escherichia coli K-12]] | ||
[[Category: Large Structures]] | |||
[[Category: Bugg TDH]] | |||
== | [[Category: Fulop V]] | ||
[[Category: Gerlt JA]] | |||
[[Category: Rakus JF]] | |||
[[Category: Escherichia coli]] | [[Category: Rea D]] | ||
[[Category: | [[Category: Roper DI]] | ||
[[Category: Bugg | |||
[[Category: Fulop | |||
[[Category: Gerlt | |||
[[Category: Rakus | |||
[[Category: Rea | |||
[[Category: Roper | |||
Latest revision as of 11:45, 15 November 2023
Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complexCrystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex
Structural highlights
FunctionRHMA_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.[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedOne 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 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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