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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Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase., Dobson RC, Griffin MD, Devenish SR, Pearce GF, Hutton CA, Gerrard JA, Jameson GB, Perugini MA, Protein Sci. 2008 Sep 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18787203 18787203]
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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 Dec 10 15:36:01 2008''
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Current revision

Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate

PDB ID 3c0j

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