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3qdk

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==Structural insight on mechanism and diverse substrate selection strategy of ribulokinase==
==Structural insight on mechanism and diverse substrate selection strategy of ribulokinase==
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<StructureSection load='3qdk' size='340' side='right' caption='[[3qdk]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
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<StructureSection load='3qdk' size='340' side='right'caption='[[3qdk]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3qdk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jvp 3jvp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QDK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3qdk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3jvp 3jvp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QDK FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=QDK:L-RIBULOSE'>QDK</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.31&#8491;</td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">araB, BH1872 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 Bacillus halodurans])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QDK:L-RIBULOSE'>QDK</scene></td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulokinase Ribulokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.16 2.7.1.16] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3qdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdk OCA], [https://pdbe.org/3qdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qdk RCSB], [https://www.ebi.ac.uk/pdbsum/3qdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qdk ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qdk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qdk RCSB], [http://www.ebi.ac.uk/pdbsum/3qdk PDBsum]</span></td></tr>
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</table>
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<table>
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== Function ==
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<div style="background-color:#fffaf0;">
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[https://www.uniprot.org/uniprot/ARAB_HALH5 ARAB_HALH5]
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== Publication Abstract from PubMed ==
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The araBAD operon encodes three different enzymes required for catabolism of L-arabinose, which is one of the most abundant monosaccharides in nature. L-ribulokinase, encoded by the araB gene, catalyzes conversion of L-ribulose to L-ribulose-5-phosphate, the second step in the catabolic pathway. Unlike other kinases, ribulokinase exhibits diversity in substrate selectivity and catalyzes phosphorylation of all four 2-ketopentose sugars with comparable k(cat) values. To understand ribulokinase recognition and phosphorylation of a diverse set of substrates, we have determined the X-ray structure of ribulokinase from Bacillus halodurans bound to L-ribulose and investigated its substrate and ATP co-factor binding properties. The polypeptide chain is folded into two domains, one small and the other large, with a deep cleft in between. By analogy with related sugar kinases, we identified (447) GGLPQK(452) as the ATP-binding motif within the smaller domain. L-ribulose binds in the cleft between the two domains via hydrogen bonds with the side chains of highly conserved Trp126, Lys208, Asp274, and Glu329 and the main chain nitrogen of Ala96. The interaction of L-ribulokinase with L-ribulose reveals versatile structural features that help explain recognition of various 2-ketopentose substrates and competitive inhibition by L-erythrulose. Comparison of our structure to that of the structures of other sugar kinases revealed conformational variations that suggest domain-domain closure movements are responsible for establishing the observed active site environment. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.
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Structural insight into mechanism and diverse substrate selection strategy of L-ribulokinase.,Agarwal R, Burley SK, Swaminathan S Proteins. 2012 Jan;80(1):261-8. doi: 10.1002/prot.23202. Epub 2011 Nov 9. PMID:22072612<ref>PMID:22072612</ref>
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus halodurans]]
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[[Category: Alkalihalobacillus halodurans]]
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[[Category: Ribulokinase]]
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[[Category: Large Structures]]
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[[Category: Agarwal, R.]]
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[[Category: Agarwal R]]
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[[Category: Burley, S K.]]
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[[Category: Burley SK]]
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[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
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[[Category: Swaminathan S]]
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[[Category: Swaminathan, S.]]
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[[Category: Arabinose catabolism]]
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[[Category: Atp binding]]
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[[Category: New york sgx research center for structural genomic]]
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[[Category: Nysgxrc]]
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[[Category: Protein structure initiative]]
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[[Category: Psi-2]]
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[[Category: Psi-ii]]
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[[Category: Structural genomic]]
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[[Category: Transferase]]
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Current revision

Structural insight on mechanism and diverse substrate selection strategy of ribulokinase

PDB ID 3qdk

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