3dfr: Difference between revisions

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-[[Image:3dfr.gif|left|200px]]<br /><applet load="3dfr" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3dfr, resolution 1.7&Aring;" />
-'''CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE'''<br />
-==Overview==
+==CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE REFINED AT 1.7 ANGSTROMS RESOLUTION. I. GENERAL FEATURES AND BINDING OF METHOTREXATE==
-X-ray data have been extended to 1.7 A for a binary complex of Escherichia coli dihydrofolate reductase with methotrexate and a ternary complex of Lactobacillus casei dihydrofolate reductase with methotrexate and NADPH. Models for both structures have been refined to R factors of 0.15 and include parameters for fixed and liquid solvent. The two species of dihydrofolate reductase resemble one another even more closely than was thought to be the case prior to refinement. Several new structural features have also been discovered. Among them are a cis peptide linking Gly-97 and Gly-98 (L. Casei numbering) in both species, an alpha helix involving residues 43 through 50 in the E. coli enzyme, and the existence of what may be a specific hydration site on exposed alpha helices. Refinement has led to a revised description of the details of methotrexate binding. We now see that a fixed water molecule mediates the interaction between methotrexate's 2-amino group and Thr-116 (L. casei numbering) and that the inhibitor's 4-amino group makes two hydrogen bonds with the enzyme (instead of one). Other revisions are also discussed. A hypothetical model for substrate binding is proposed in which the pteridine ring is turned upside down while all protein and solvent atoms remain fixed. Asp-26 in this model is hydrogen bonded to the substrate's 2-amino group and to N3.
+<StructureSection load='3dfr' size='340' side='right'caption='[[3dfr]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3dfr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lacticaseibacillus_casei Lacticaseibacillus casei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dfr 1dfr]. The October 2002 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Dihydrofolate Reductase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2002_10 10.2210/rcsb_pdb/mom_2002_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DFR 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]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTX:METHOTREXATE'>MTX</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=3dfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dfr OCA], [https://pdbe.org/3dfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dfr RCSB], [https://www.ebi.ac.uk/pdbsum/3dfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dfr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DYR_LACCA DYR_LACCA] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis.
+== 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/df/3dfr_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=3dfr ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-DFR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei] with <scene name='pdbligand=NDP:'>NDP</scene> and <scene name='pdbligand=MTX:'>MTX</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1DFR. The following page contains interesting information on the relation of 3DFR with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb34_1.html Dihydrofolate Reductase]]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DFR OCA].
+*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate., Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J, J Biol Chem. 1982 Nov 25;257(22):13650-62. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=6815178 6815178]
 [[Category: Dihydrofolate Reductase]]
-[[Category: Dihydrofolate reductase]]
+[[Category: Lacticaseibacillus casei]]
-[[Category: Lactobacillus casei]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Bolin, J T.]]
+[[Category: Bolin JT]]
-[[Category: Filman, D J.]]
+[[Category: Filman DJ]]
-[[Category: Kraut, J.]]
+[[Category: Kraut J]]
-[[Category: Matthews, D A.]]
+[[Category: Matthews DA]]
-[[Category: MTX]]
-[[Category: NDP]]
-[[Category: oxido-reductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:09:02 2008''