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| | ==Structure of oxidized Deinococcus radiodurans proline dehydrogenase complexed with L-tetrahydrofuroic acid== | | ==Structure of oxidized Deinococcus radiodurans proline dehydrogenase complexed with L-tetrahydrofuroic acid== |
| - | <StructureSection load='4h6q' size='340' side='right' caption='[[4h6q]], [[Resolution|resolution]] 1.36Å' scene=''> | + | <StructureSection load='4h6q' size='340' side='right'caption='[[4h6q]], [[Resolution|resolution]] 1.36Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4h6q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans_r1 Deinococcus radiodurans r1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H6Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H6Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4h6q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H6Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H6Q FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TFB:TETRAHYDROFURAN-2-CARBOXYLIC+ACID'>TFB</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.359Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4h6r|4h6r]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=TFB:TETRAHYDROFURAN-2-CARBOXYLIC+ACID'>TFB</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_0814, PROLINE DEHYDROGENASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 Deinococcus radiodurans R1])</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=4h6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h6q OCA], [https://pdbe.org/4h6q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h6q RCSB], [https://www.ebi.ac.uk/pdbsum/4h6q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h6q ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </span></td></tr> | + | |
| - | <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=4h6q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h6q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h6q RCSB], [http://www.ebi.ac.uk/pdbsum/4h6q PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PRODH_DEIRA PRODH_DEIRA] Converts proline to delta-1-pyrroline-5-carboxylate.<ref>PMID:23151026</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4h6q" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Proline utilization A|Proline utilization A]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deinococcus radiodurans r1]] | + | [[Category: Deinococcus radiodurans R1]] |
| - | [[Category: Proline dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Min, L]] | + | [[Category: Min L]] |
| - | [[Category: Tanner, J J]] | + | [[Category: Tanner JJ]] |
| - | [[Category: Beta8-alpha8-barrel]]
| + | |
| - | [[Category: Flavoenzyme]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
PRODH_DEIRA Converts proline to delta-1-pyrroline-5-carboxylate.[1]
Publication Abstract from PubMed
Proline dehydrogenase catalyzes the FAD-dependent oxidation of proline to Delta1- pyrroline-5-carboxylate, which is the first step of proline catabolism. Here, we report the structures of proline dehydrogenase from Deinococcus radiodurans in the oxidized state complexed with the proline analog L-tetrahydrofuroic acid and in the reduced state with the proline site vacant. The analog binds against the si face of the FAD isoalloxazine and is protected from bulk solvent by the alpha8 helix and the beta1-alpha1 loop. The FAD ribityl chain adopts two conformations in the E-S complex, which is unprecedented for flavoenzymes. One of the conformations is novel for the PRODH superfamily and may contribute to the low substrate affinity of Deinococcus PRODH. Reduction of the crystalline enzyme-inhibitor complex causes profound structural changes, including 20 degrees butterfly bending of the isoalloxazine, crankshaft rotation of the ribityl, shifting of alpha8 by 1.7 A, reconfiguration of the beta1-alpha1 loop, and rupture of the Arg291-Glu64 ion pair. These changes dramatically open the active site to facilitate product release and allow electron acceptors access to the reduced flavin. The structures suggest that the ion pair, which is conserved in the PRODH superfamily, functions as the active site gate. Mutagenesis of Glu64 to Ala decreases catalytic efficiency 27-fold, which demonstrates the importance of the gate. Mutation of Gly63 decreases efficiency 140-fold, which suggests that flexibility of the beta1-alpha1 loop is essential for optimal catalysis. The large conformational changes that are required to form the E-S complex suggest that conformational selection plays a role in substrate recognition.
Crystal Structures and Kinetics of Monofunctional Proline Dehydrogenase Provide Insight into Substrate Recognition and Conformational Changes Associated With Flavin Reduction and Product Release.,Luo M, Arentson BW, Srivastava D, Becker DF, Tanner JJ Biochemistry. 2012 Nov 14. PMID:23151026[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Luo M, Arentson BW, Srivastava D, Becker DF, Tanner JJ. Crystal Structures and Kinetics of Monofunctional Proline Dehydrogenase Provide Insight into Substrate Recognition and Conformational Changes Associated With Flavin Reduction and Product Release. Biochemistry. 2012 Nov 14. PMID:23151026 doi:http://dx.doi.org/10.1021/bi301312f
- ↑ Luo M, Arentson BW, Srivastava D, Becker DF, Tanner JJ. Crystal Structures and Kinetics of Monofunctional Proline Dehydrogenase Provide Insight into Substrate Recognition and Conformational Changes Associated With Flavin Reduction and Product Release. Biochemistry. 2012 Nov 14. PMID:23151026 doi:http://dx.doi.org/10.1021/bi301312f
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