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3uyi

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Crystal Structure of Perakine Reductase, Founder Member of a Novel AKR Subfamily with Unique Conformational Changes during NADPH Binding

Structural highlights

3uyi is a 1 chain structure with sequence from Rauvolfia serpentina. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.313Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PERR_RAUSE Aldo-keto reductase involved in the biosynthesis of monoterpenoid indole alkaloids. Broad substrate specificity enzyme with a high selectivity in the group of alkaloids. Can use perakine, 19(S),20(R)-dihydro-peraksine-17,21-al, cinnamic aldehyde, p-coumaric aldehyde and 3-(3,4,5-trimethoxyphenyl)propanal as substrates, but not ketosteroids such as progesterone. NADPH could not be replaced by NADH.^[1]

Publication Abstract from PubMed

Perakine reductase (PR) catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. Sequence alignment shows that PR is the founder of the new AKR13D subfamily and is designated AKR13D1. The x-ray structure of methylated His(6)-PR was solved to 2.31 A. However, the active site of PR was blocked by the connected parts of the neighbor symmetric molecule in the crystal. To break the interactions and obtain the enzyme-ligand complexes, the A213W mutant was generated. The atomic structure of His(6)-PR-A213W complex with NADPH was determined at 1.77 A. Overall, PR folds in an unusual alpha(8)/beta(6) barrel that has not been observed in any other AKR protein to date. NADPH binds in an extended pocket, but the nicotinamide riboside moiety is disordered. Upon NADPH binding, dramatic conformational changes and movements were observed: two additional beta-strands in the C terminus become ordered to form one alpha-helix, and a movement of up to 24 A occurs. This conformational change creates a large space that allows the binding of substrates of variable size for PR and enhances the enzyme activity; as a result cooperative kinetics are observed as NADPH is varied. As the founding member of the new AKR13D subfamily, PR also provides a structural template and model of cofactor binding for the AKR13 family.

Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding.,Sun L, Chen Y, Rajendran C, Mueller U, Panjikar S, Wang M, Mindnich R, Rosenthal C, Penning TM, Stockigt J J Biol Chem. 2012 Mar 30;287(14):11213-21. Epub 2012 Feb 13. PMID:22334702^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sun L, Ruppert M, Sheludko Y, Warzecha H, Zhao Y, Stockigt J. Purification, cloning, functional expression and characterization of perakine reductase: the first example from the AKR enzyme family, extending the alkaloidal network of the plant Rauvolfia. Plant Mol Biol. 2008 Jul;67(5):455-67. doi: 10.1007/s11103-008-9331-7. Epub 2008 , Apr 13. PMID:18409028 doi:10.1007/s11103-008-9331-7
↑ Sun L, Chen Y, Rajendran C, Mueller U, Panjikar S, Wang M, Mindnich R, Rosenthal C, Penning TM, Stockigt J. Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding. J Biol Chem. 2012 Mar 30;287(14):11213-21. Epub 2012 Feb 13. PMID:22334702 doi:10.1074/jbc.M111.335521

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3uyi"

@@ Line 3: / Line 3: @@
 <StructureSection load='3uyi' size='340' side='right'caption='[[3uyi]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3uyi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ophioxylon_serpentinum Ophioxylon serpentinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UYI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3uyi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rauvolfia_serpentina Rauvolfia serpentina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UYI FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</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]] 2.313&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4060 Ophioxylon serpentinum])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</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=3uyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uyi OCA], [https://pdbe.org/3uyi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uyi RCSB], [https://www.ebi.ac.uk/pdbsum/3uyi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uyi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PERR_RAUSE PERR_RAUSE]] Aldo-keto reductase involved in the biosynthesis of monoterpenoid indole alkaloids. Broad substrate specificity enzyme with a high selectivity in the group of alkaloids. Can use perakine, 19(S),20(R)-dihydro-peraksine-17,21-al, cinnamic aldehyde, p-coumaric aldehyde and 3-(3,4,5-trimethoxyphenyl)propanal as substrates, but not ketosteroids such as progesterone. NADPH could not be replaced by NADH.<ref>PMID:18409028</ref>
+[https://www.uniprot.org/uniprot/PERR_RAUSE PERR_RAUSE] Aldo-keto reductase involved in the biosynthesis of monoterpenoid indole alkaloids. Broad substrate specificity enzyme with a high selectivity in the group of alkaloids. Can use perakine, 19(S),20(R)-dihydro-peraksine-17,21-al, cinnamic aldehyde, p-coumaric aldehyde and 3-(3,4,5-trimethoxyphenyl)propanal as substrates, but not ketosteroids such as progesterone. NADPH could not be replaced by NADH.<ref>PMID:18409028</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Ophioxylon serpentinum]]
+[[Category: Rauvolfia serpentina]]
-[[Category: Chen, Y]]
+[[Category: Chen Y]]
-[[Category: Mindnich, R]]
+[[Category: Mindnich R]]
-[[Category: Mueller, U]]
+[[Category: Mueller U]]
-[[Category: Panjikar, S]]
+[[Category: Panjikar S]]
-[[Category: Penning, T M]]
+[[Category: Penning TM]]
-[[Category: Rajendran, C]]
+[[Category: Rajendran C]]
-[[Category: Rosenthal, C]]
+[[Category: Rosenthal C]]
-[[Category: Stoeckigt, J]]
+[[Category: Stoeckigt J]]
-[[Category: Sun, L]]
+[[Category: Sun L]]
-[[Category: Wang, M]]
+[[Category: Wang M]]
-[[Category: 8/6 barrel]]
-[[Category: Akr superfamily]]
-[[Category: Nadph]]
-[[Category: Oxidoreductase]]
-[[Category: Perakine reductase]]

3uyi

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Current revision

Crystal Structure of Perakine Reductase, Founder Member of a Novel AKR Subfamily with Unique Conformational Changes during NADPH Binding

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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