1pr9: Difference between revisions

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<StructureSection load='1pr9' size='340' side='right'caption='[[1pr9]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
<StructureSection load='1pr9' size='340' side='right'caption='[[1pr9]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1pr9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PR9 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1pr9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PR9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.96&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-xylulose_reductase L-xylulose reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.10 1.1.1.10] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2HP:DIHYDROGENPHOSPHATE+ION'>2HP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=1pr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pr9 OCA], [https://pdbe.org/1pr9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pr9 RCSB], [https://www.ebi.ac.uk/pdbsum/1pr9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pr9 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=1pr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pr9 OCA], [https://pdbe.org/1pr9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pr9 RCSB], [https://www.ebi.ac.uk/pdbsum/1pr9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pr9 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
== Disease ==
[[https://www.uniprot.org/uniprot/DCXR_HUMAN DCXR_HUMAN]] Note=The enzyme defect in pentosuria has been shown to involve L-xylulose reductase. Essential pentosuria is an inborn error of metabolism characterized by the excessive urinary excretion of the pentose L-xylulose.  
[https://www.uniprot.org/uniprot/DCXR_HUMAN DCXR_HUMAN] Note=The enzyme defect in pentosuria has been shown to involve L-xylulose reductase. Essential pentosuria is an inborn error of metabolism characterized by the excessive urinary excretion of the pentose L-xylulose.
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/DCXR_HUMAN DCXR_HUMAN]] Catalyzes the NADPH-dependent reduction of several pentoses, tetroses, trioses, alpha-dicarbonyl compounds and L-xylulose. Participates in the uronate cycle of glucose metabolism. May play a role in the water absorption and cellular osmoregulation in the proximal renal tubules by producing xylitol, an osmolyte, thereby preventing osmolytic stress from occurring in the renal tubules.  
[https://www.uniprot.org/uniprot/DCXR_HUMAN DCXR_HUMAN] Catalyzes the NADPH-dependent reduction of several pentoses, tetroses, trioses, alpha-dicarbonyl compounds and L-xylulose. Participates in the uronate cycle of glucose metabolism. May play a role in the water absorption and cellular osmoregulation in the proximal renal tubules by producing xylitol, an osmolyte, thereby preventing osmolytic stress from occurring in the renal tubules.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1pr9 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=1pr9 ConSurf].
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== Publication Abstract from PubMed ==
L-Xylulose reductase (XR), an enzyme in the uronate cycle of glucose metabolism, belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. Among the SDR enzymes, XR shows the highest sequence identity (67%) with mouse lung carbonyl reductase (MLCR), but the two enzymes show different substrate specificities. The crystal structure of human XR in complex with reduced nicotinamide adenine dinucleotide phosphate (NADPH) was determined at 1.96 A resolution by using the molecular replacement method and the structure of MLCR as the search model. Features unique to human XR include electrostatic interactions between the N-terminal residues of subunits related by the P-axis, termed according to SDR convention, and an interaction between the hydroxy group of Ser185 and the pyrophosphate of NADPH. Furthermore, identification of the residues lining the active site of XR (Cys138, Val143, His146, Trp191, and Met200) together with a model structure of XR in complex with L-xylulose, revealed structural differences with other members of the SDR family, which may account for the distinct substrate specificity of XR. The residues comprising a recently proposed catalytic tetrad in the SDR enzymes are conserved in human XR (Asn107, Ser136, Tyr149, and Lys153). To examine the role of Asn107 in the catalytic mechanism of human XR, mutant forms (N107D and N107L) were prepared. The two mutations increased K(m) for the substrate (&gt;26-fold) and K(d) for NADPH (95-fold), but only the N107L mutation significantly decreased k(cat) value. These results suggest that Asn107 plays a critical role in coenzyme binding rather than in the catalytic mechanism.
Crystal structure of human L-xylulose reductase holoenzyme: probing the role of Asn107 with site-directed mutagenesis.,El-Kabbani O, Ishikura S, Darmanin C, Carbone V, Chung RP, Usami N, Hara A Proteins. 2004 May 15;55(3):724-32. PMID:15103634<ref>PMID:15103634</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1pr9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: L-xylulose reductase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Carbone, V]]
[[Category: Carbone V]]
[[Category: Chung, R P.T]]
[[Category: Chung RP-T]]
[[Category: Darmanin, C]]
[[Category: Darmanin C]]
[[Category: El-Kabbani, O]]
[[Category: El-Kabbani O]]
[[Category: Hara, A]]
[[Category: Hara A]]
[[Category: Ishikura, S]]
[[Category: Ishikura S]]
[[Category: Usami, N]]
[[Category: Usami N]]
[[Category: Dinucleotide binding domain]]
[[Category: Oxidoreductase]]
[[Category: Short chain dehydrogenase/reductase]]
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