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4gh8

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==Crystal structure of a 'humanized' E. coli dihydrofolate reductase==
==Crystal structure of a 'humanized' E. coli dihydrofolate reductase==
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<StructureSection load='4gh8' size='340' side='right' caption='[[4gh8]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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<StructureSection load='4gh8' size='340' side='right'caption='[[4gh8]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gh8]] is a 2 chain structure with sequence from [http://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=4GH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GH8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gh8]] 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=4GH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GH8 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MTX:METHOTREXATE'>MTX</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]] 1.85&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">folA, tmrA, b0048, JW0047 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MTX:METHOTREXATE'>MTX</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4gh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gh8 OCA], [https://pdbe.org/4gh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gh8 RCSB], [https://www.ebi.ac.uk/pdbsum/4gh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gh8 ProSAT]</span></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=4gh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gh8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gh8 RCSB], [http://www.ebi.ac.uk/pdbsum/4gh8 PDBsum]</span></td></tr>
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</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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With the rapidly growing wealth of genomic data, experimental inquiries on the functional significance of important divergence sites in protein evolution are becoming more accessible. Here we trace the evolution of dihydrofolate reductase (DHFR) and identify multiple key divergence sites among 233 species between humans and bacteria. We connect these sites, experimentally and computationally, to changes in the enzyme's binding properties and catalytic efficiency. One of the identified evolutionarily important sites is the N23PP modification ( approximately mid-Devonian, 415-385 Mya), which alters the conformational states of the active site loop in Escherichia coli dihydrofolate reductase and negatively impacts catalysis. This enzyme activity was restored with the inclusion of an evolutionarily significant lid domain (G51PEKN in E. coli enzyme; approximately 2.4 Gya). Guided by this evolutionary genomic analysis, we generated a human-like E. coli dihydrofolate reductase variant through three simple mutations despite only 26% sequence identity between native human and E. coli DHFRs. Molecular dynamics simulations indicate that the overall conformational motions of the protein within a common scaffold are retained throughout evolution, although subtle changes to the equilibrium conformational sampling altered the free energy barrier of the enzymatic reaction in some cases. The data presented here provide a glimpse into the evolutionary trajectory of functional DHFR through its protein sequence space that lead to the diverged binding and catalytic properties of the E. coli and human enzymes.
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Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans.,Liu CT, Hanoian P, French JB, Pringle TH, Hammes-Schiffer S, Benkovic SJ Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10159-64. doi:, 10.1073/pnas.1307130110. Epub 2013 Jun 3. PMID:23733948<ref>PMID:23733948</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: Escherichia coli k-12]]
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[[Category: Large Structures]]
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[[Category: Benkovic, S J]]
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[[Category: Benkovic SJ]]
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[[Category: French, J B]]
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[[Category: French JB]]
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[[Category: Hammes-Schiffer, S]]
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[[Category: Hammes-Schiffer S]]
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[[Category: Hanoian, P]]
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[[Category: Hanoian P]]
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[[Category: Liu, C T]]
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[[Category: Liu CT]]
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[[Category: Pringle, T H]]
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[[Category: Pringle TH]]
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[[Category: Enzyme catalysis]]
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[[Category: Evolution]]
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[[Category: Oxidoreductase]]
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[[Category: Tetrahydrofolate]]
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Current revision

Crystal structure of a 'humanized' E. coli dihydrofolate reductase

PDB ID 4gh8

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