3c0j

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{{Seed}}
 
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[[Image:3c0j.png|left|200px]]
 
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==Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate==
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The line below this paragraph, containing "STRUCTURE_3c0j", creates the "Structure Box" on the page.
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<StructureSection load='3c0j' size='340' side='right'caption='[[3c0j]], [[Resolution|resolution]] 2.40&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'>[[3c0j]] is a 2 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=3C0J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C0J 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]] 2.4&#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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=KYQ:(E)-N~6~-(1-CARBOXY-2-HYDROXYETHYLIDENE)-L-LYSINE'>KYQ</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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{{STRUCTURE_3c0j| PDB=3c0j | 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=3c0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c0j OCA], [https://pdbe.org/3c0j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c0j RCSB], [https://www.ebi.ac.uk/pdbsum/3c0j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c0j ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DAPA_ECOLI DAPA_ECOLI] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).<ref>PMID:20503968</ref> <ref>PMID:8993314</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/c0/3c0j_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3c0j 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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In recent years, dihydrodipicolinate synthase (DHDPS, E.C. 4.2.1.52) has received considerable attention from a mechanistic and structural viewpoint. DHDPS catalyzes the reaction of (S)-aspartate-beta-semialdehyde with pyruvate, which is bound via a Schiff base to a conserved active-site lysine (Lys161 in the enzyme from Escherichia coli). To probe the mechanism of DHDPS, we have studied the inhibition of E. coli DHDPS by the substrate analog, beta-hydroxypyruvate. The K (i) was determined to be 0.21 (+/-0.02) mM, similar to that of the allosteric inhibitor, (S)-lysine, and beta-hydroxypyruvate was observed to cause time-dependent inhibition. The inhibitory reaction with beta-hydroxypyruvate could be qualitatively followed by mass spectrometry, which showed initial noncovalent adduct formation, followed by the slow formation of the covalent adduct. It is unclear whether beta-hydroxypyruvate plays a role in regulating the biosynthesis of meso-diaminopimelate and (S)-lysine in E. coli, although we note that it is present in vivo. The crystal structure of DHDPS complexed with beta-hydroxypyruvate was solved. The active site clearly showed the presence of the inhibitor covalently bound to the Lys161. Interestingly, the hydroxyl group of beta-hydroxypyruvate was hydrogen-bonded to the main-chain carbonyl of Ile203. This provides insight into the possible catalytic role played by this peptide unit, which has a highly strained torsion angle (omega approximately 201 degrees ). A survey of the known DHDPS structures from other organisms shows this distortion to be a highly conserved feature of the DHDPS active site, and we propose that this peptide unit plays a critical role in catalysis.
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===Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate===
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Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase.,Dobson RC, Griffin MD, Devenish SR, Pearce FG, Hutton CA, Gerrard JA, Jameson GB, Perugini MA Protein Sci. 2008 Dec;17(12):2080-90. Epub 2008 Sep 11. PMID:18787203<ref>PMID:18787203</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 3c0j" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18787203}}, adds the Publication Abstract to the page
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*[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18787203 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18787203}}
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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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3C0J 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=3C0J OCA].
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[[Category: Large Structures]]
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[[Category: Dobson RCJ]]
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==Reference==
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<ref group="xtra">PMID:18787203</ref><references group="xtra"/>
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[[Category: Dihydrodipicolinate synthase]]
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[[Category: Escherichia coli]]
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[[Category: Dobson, R C.J.]]
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[[Category: Amino-acid biosynthesis]]
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[[Category: Cytoplasm]]
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[[Category: Diaminopimelate biosynthesis]]
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[[Category: Dihydrodipicolinate synthase]]
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[[Category: Lyase]]
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[[Category: Lysine biosynthase]]
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[[Category: Lysine biosynthesis]]
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[[Category: Schiff base]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:09:40 2009''
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Current revision

Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate

PDB ID 3c0j

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