6a8c: Difference between revisions
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<StructureSection load='6a8c' size='340' side='right'caption='[[6a8c]], [[Resolution|resolution]] 1.98Å' scene=''> | <StructureSection load='6a8c' size='340' side='right'caption='[[6a8c]], [[Resolution|resolution]] 1.98Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6a8c]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A8C OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6a8c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_donovani_BPK282A1 Leishmania donovani BPK282A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A8C FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.98Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6a8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8c OCA], [https://pdbe.org/6a8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a8c RCSB], [https://www.ebi.ac.uk/pdbsum/6a8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8c ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/A0A3S7X0F5_LEIDO A0A3S7X0F5_LEIDO] Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.[HAMAP-Rule:MF_03215] | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ribokinase (RK) is an ATP dependent sugar kinase that enables the entry of ribose in the metabolism. Leishmania accumulates ribose into the cytosol through hydrolysis of nucleosides and by transport from the extracellular environment. Activation by RK is critical to mobilize the ribose into the metabolism of Leishmania. To understand the catalytic role, the crystal structure of RK (LdRK) from L. donovani was determined in the apo and complex forms with several nucleotides (ATP, AMPPCP and ADP) in the presence of Na(+) ion. The dual insertion of five amino acid stretches makes LdRK structurally unique from other reported structures of RKs. The structure of LdRK-ATP provided the basis for positioning of gamma-phosphate of ATP by conserved -GAGD- motif. Liganded and unliganded structures of LdRK exists in similar conformation, which suggests binding of nucleotides does not make any significant conformational changes in nucleotide-bound structures. Substitution of a conserved asparagine with phenylalanine in ribose binding pocket differentiates the LdRK from other RKs. Glycerol molecule bound in the substrate binding pocket mimics the enzyme-substrate interactions but in turn, hampers the binding of ribose to LdRK. Comparative structural analysis revealed the flexibility of gamma-phosphate, which adopts multiple conformations in the absence of divalent metal ion and ribose. Similar to other RKs, LdRK is also dependent on monovalent as well as divalent cations for its catalytic activity. | |||
Unraveling structural insights of ribokinase from Leishmania donovani.,Gatreddi S, Pillalamarri V, Vasudevan D, Addlagatta A, Qureshi IA Int J Biol Macromol. 2019 Sep 1;136:253-265. doi: 10.1016/j.ijbiomac.2019.06.001. , Epub 2019 Jun 3. PMID:31170491<ref>PMID:31170491</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6a8c" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Ribokinase 3D structures|Ribokinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Leishmania donovani BPK282A1]] | ||
[[Category: Gatreddi | [[Category: Gatreddi S]] | ||
[[Category: Qureshi | [[Category: Qureshi IA]] | ||
[[Category: Vasudevan | [[Category: Vasudevan D]] | ||
Latest revision as of 12:21, 22 November 2023
Ribokinase from Leishmania donovani with ADPRibokinase from Leishmania donovani with ADP
Structural highlights
FunctionA0A3S7X0F5_LEIDO Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway.[HAMAP-Rule:MF_03215] Publication Abstract from PubMedRibokinase (RK) is an ATP dependent sugar kinase that enables the entry of ribose in the metabolism. Leishmania accumulates ribose into the cytosol through hydrolysis of nucleosides and by transport from the extracellular environment. Activation by RK is critical to mobilize the ribose into the metabolism of Leishmania. To understand the catalytic role, the crystal structure of RK (LdRK) from L. donovani was determined in the apo and complex forms with several nucleotides (ATP, AMPPCP and ADP) in the presence of Na(+) ion. The dual insertion of five amino acid stretches makes LdRK structurally unique from other reported structures of RKs. The structure of LdRK-ATP provided the basis for positioning of gamma-phosphate of ATP by conserved -GAGD- motif. Liganded and unliganded structures of LdRK exists in similar conformation, which suggests binding of nucleotides does not make any significant conformational changes in nucleotide-bound structures. Substitution of a conserved asparagine with phenylalanine in ribose binding pocket differentiates the LdRK from other RKs. Glycerol molecule bound in the substrate binding pocket mimics the enzyme-substrate interactions but in turn, hampers the binding of ribose to LdRK. Comparative structural analysis revealed the flexibility of gamma-phosphate, which adopts multiple conformations in the absence of divalent metal ion and ribose. Similar to other RKs, LdRK is also dependent on monovalent as well as divalent cations for its catalytic activity. Unraveling structural insights of ribokinase from Leishmania donovani.,Gatreddi S, Pillalamarri V, Vasudevan D, Addlagatta A, Qureshi IA Int J Biol Macromol. 2019 Sep 1;136:253-265. doi: 10.1016/j.ijbiomac.2019.06.001. , Epub 2019 Jun 3. PMID:31170491[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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