1dr1
From Proteopedia
(Difference between revisions)
Line 3: | Line 3: | ||
<StructureSection load='1dr1' size='340' side='right'caption='[[1dr1]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='1dr1' size='340' side='right'caption='[[1dr1]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
- | <table><tr><td colspan='2'>[[1dr1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1dr1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DR1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DR1 FirstGlance]. <br> |
- | </td></tr><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=HBI:7,8-DIHYDROBIOPTERIN'>HBI</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
- | + | <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=HBI:7,8-DIHYDROBIOPTERIN'>HBI</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=1dr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dr1 OCA], [https://pdbe.org/1dr1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dr1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dr1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dr1 ProSAT]</span></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=1dr1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dr1 OCA], [https://pdbe.org/1dr1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dr1 RCSB], [https://www.ebi.ac.uk/pdbsum/1dr1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dr1 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
- | + | [https://www.uniprot.org/uniprot/DYR_CHICK DYR_CHICK] Key enzyme in folate metabolism. Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis. May bind to mRNA. | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Line 20: | Line 20: | ||
</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=1dr1 ConSurf]. | </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=1dr1 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
- | <div style="background-color:#fffaf0;"> | ||
- | == Publication Abstract from PubMed == | ||
- | The 2.2-A crystal structure of chicken liver dihydrofolate reductase (EC 1.5.1.3, DHFR) has been solved as a ternary complex with NADP+ and biopterin (a poor substrate). The space group and unit cell are isomorphous with the previously reported structure of chicken liver DHFR complexed with NADPH and phenyltriazine [Volz, K. W., Matthews, D. A., Alden, R. A., Freer, S. T., Hansch, C., Kaufman, B. T., & Kraut, J. (1982) J. Biol. Chem. 257, 2528-2536]. The structure contains an ordered water molecule hydrogen-bonded to both hydroxyls of the biopterin dihydroxypropyl group as well as to O4 and N5 of the biopterin pteridine ring. This water molecule, not observed in previously determined DHFR structures, is positioned to complete a proposed route for proton transfer from the side-chain carboxylate of E30 to N5 of the pteridine ring. Protonation of N5 is believed to occur during the reduction of dihydropteridine substrates. The positions of the NADP+ nicotinamide and biopterin pteridine rings are quite similar to the nicotinamide and pteridine ring positions in the Escherichia coli DHFR.NADP+.folate complex [Bystroff, C., Oatley, S. J., & Kraut, J. (1990) Biochemistry 29, 3263-3277], suggesting that the reduction of biopterin and the reduction of folate occur via similar mechanisms, that the binding geometry of the nicotinamide and pteridine rings is conserved between DHFR species, and that the p-aminobenzoylglutamate moiety of folate is not required for correct positioning of the pteridine ring in ground-state ternary complexes. Instead, binding of the p-aminobenzoylglutamate moiety of folate may induce the side chain of residue 31 (tyrosine or phenylalanine) in vertebrate DHFRs to adopt a conformation in which the opening to the pteridine binding site is too narrow to allow the substrate to diffuse away rapidly. A reverse conformational change of residue 31 is proposed to be required for tetrahydrofolate release. | ||
- | |||
- | Crystal structure of chicken liver dihydrofolate reductase complexed with NADP+ and biopterin.,McTigue MA, Davies JF 2nd, Kaufman BT, Kraut J Biochemistry. 1992 Aug 18;31(32):7264-73. PMID:1510919<ref>PMID:1510919</ref> | ||
- | |||
- | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
- | </div> | ||
- | <div class="pdbe-citations 1dr1" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]] | *[[Dihydrofolate reductase 3D structures|Dihydrofolate reductase 3D structures]] | ||
- | == References == | ||
- | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
- | [[Category: | + | [[Category: Gallus gallus]] |
- | + | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
- | [[Category: /II | + | [[Category: Davies /II JF]] |
- | [[Category: Kaufman | + | [[Category: Kaufman BT]] |
- | [[Category: Kraut | + | [[Category: Kraut J]] |
- | [[Category: Mctigue | + | [[Category: Mctigue MA]] |
- | [[Category: Xuong | + | [[Category: Xuong N-H]] |
- | + |
Current revision
2.2 ANGSTROMS CRYSTAL STRUCTURE OF CHICKEN LIVER DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADP+ AND BIOPTERIN
|