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3r33

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==Evidence for dynamic motion in proteins as a mechanism for ligand dissociation==
==Evidence for dynamic motion in proteins as a mechanism for ligand dissociation==
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<StructureSection load='3r33' size='340' side='right' caption='[[3r33]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
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<StructureSection load='3r33' size='340' side='right'caption='[[3r33]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3r33]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R33 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R33 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3r33]] is a 1 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=3R33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R33 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6ME:(6S)-6-METHYL-5,6,7,8-TETRAHYDROQUINAZOLINE-2,4-DIAMINE'>6ME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
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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]] 2.09&#8491;</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </span></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=6ME:(6S)-6-METHYL-5,6,7,8-TETRAHYDROQUINAZOLINE-2,4-DIAMINE'>6ME</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3r33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r33 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r33 RCSB], [http://www.ebi.ac.uk/pdbsum/3r33 PDBsum]</span></td></tr>
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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=3r33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r33 OCA], [https://pdbe.org/3r33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r33 RCSB], [https://www.ebi.ac.uk/pdbsum/3r33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r33 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
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[https://www.uniprot.org/uniprot/DYR_ECOLI DYR_ECOLI] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Signal transduction, regulatory processes and pharmaceutical responses are highly dependent upon ligand residence times. Gaining insight into how physical factors influence residence times (1/k(off)) should enhance our ability to manipulate biological interactions. We report experiments that yield structural insight into k(off) involving a series of eight 2,4-diaminopyrimidine inhibitors of dihydrofolate reductase whose binding affinities vary by six orders of magnitude. NMR relaxation-dispersion experiments revealed a common set of residues near the binding site that undergo a concerted millisecond-timescale switching event to a previously unidentified conformation. The rate of switching from ground to excited conformations correlates exponentially with the binding affinity K(i) and k(off), suggesting that protein dynamics serves as a mechanical initiator of ligand dissociation within this series and potentially for other macromolecule-ligand systems. Although the forward rate of conformational exchange, k(conf,forward), is faster than k(off), the use of the ligand series allowed for connections to be drawn between kinetic events on different timescales.
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Evidence for dynamics in proteins as a mechanism for ligand dissociation.,Carroll MJ, Mauldin RV, Gromova AV, Singleton SF, Collins EJ, Lee AL Nat Chem Biol. 2012 Jan 15;8(3):246-52. doi: 10.1038/nchembio.769. PMID:22246400<ref>PMID:22246400</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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==See Also==
==See Also==
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*[[Dihydrofolate reductase|Dihydrofolate reductase]]
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*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Dihydrofolate reductase]]
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[[Category: Escherichia coli K-12]]
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[[Category: Ecoli]]
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[[Category: Large Structures]]
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[[Category: Carroll, M J]]
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[[Category: Carroll MJ]]
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[[Category: Collins, E J]]
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[[Category: Collins EJ]]
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[[Category: Gromova, A V]]
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[[Category: Gromova AV]]
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[[Category: Lee, A L]]
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[[Category: Lee AL]]
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[[Category: Mauldin, R V]]
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[[Category: Mauldin RV]]
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[[Category: Singleton, S F]]
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[[Category: Singleton SF]]
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[[Category: Oxidoreductase]]
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[[Category: Reductase]]
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[[Category: Rossmann fold]]
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Current revision

Evidence for dynamic motion in proteins as a mechanism for ligand dissociation

PDB ID 3r33

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