This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3b1n

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:51, 11 October 2023

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with ADP-mizoribine

Structural highlights

3b1n is a 2 chain structure with sequence from Burkholderia thailandensis E264. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.55Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q2SZE4_BURTA

Publication Abstract from PubMed

The nucleoside kinase (NK) from the mesophilic Gram-negative bacterium Burkholderia thailandensis (BthNK) is a member of the phosphofructokinase B (Pfk-B) family and catalyzes the Mg(2+)- and ATP-dependent phosphorylation of a broad range of nucleosides such as inosine (INO), adenosine (ADO) and mizoribine (MZR). BthNK is currently used in clinical practice to measure serum MZR levels. Here, crystal structures of BthNK in a ligand-free form and in complexes with INO, INO-ADP, MZR-ADP and AMP-Mg(2+)-AMP are described. The typical homodimeric architecture of Pfk-B enzymes was detected in three distinct conformational states: an asymmetric dimer with one subunit in an open conformation and the other in a closed conformation (the ligand-free form), a closed conformation (the binary complex with INO) and a fully closed conformation (the other ternary and quaternary complexes). The previously unreported fully closed structures suggest the possibility that Mg(2+) might directly interact with the beta- and gamma-phosphates of ATP to maintain neutralization of the negative charge throughout the reaction. The nucleoside-complex structures also showed that the base moiety of the bound nucleoside is partly exposed to the solvent, thereby enabling the recognition of a wide range of nucleoside bases. Gly170 is responsible for the solvent accessibility of the base moiety and is assumed to be a key residue for the broad nucleoside recognition of BthNK. Remarkably, the G170Q mutation increases the specificity of BthNK for ADO. These findings provide insight into the conformational dynamics, catalytic mechanism and nucleoside selectivity of BthNK and related enzymes.

Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity.,Yasutake Y, Ota H, Hino E, Sakasegawa S, Tamura T Acta Crystallogr D Biol Crystallogr. 2011 Nov;67(Pt 11):945-56. Epub 2011 Oct 19. PMID:22101821^[1]

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

References

↑ Yasutake Y, Ota H, Hino E, Sakasegawa S, Tamura T. Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity. Acta Crystallogr D Biol Crystallogr. 2011 Nov;67(Pt 11):945-56. Epub 2011 Oct 19. PMID:22101821 doi:10.1107/S0907444911038777

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/3b1n"

@@ Line 3: / Line 3: @@
 <StructureSection load='3b1n' size='340' side='right'caption='[[3b1n]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3b1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burta Burta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B1N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3b1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_thailandensis_E264 Burkholderia thailandensis E264]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B1N FirstGlance]. <br>
-</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MZR:5-HYDROXY-1-(BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXAMIDE'>MZR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.55&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3b1o|3b1o]], [[3b1p|3b1p]], [[3b1q|3b1q]], [[3b1r|3b1r]]</div></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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MZR:5-HYDROXY-1-(BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXAMIDE'>MZR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BTH_I1158 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271848 BURTA])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diphosphate-purine_nucleoside_kinase Diphosphate-purine nucleoside kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.143 2.7.1.143] </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=3b1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b1n OCA], [https://pdbe.org/3b1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b1n RCSB], [https://www.ebi.ac.uk/pdbsum/3b1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b1n ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q2SZE4_BURTA Q2SZE4_BURTA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Burta]]
+[[Category: Burkholderia thailandensis E264]]
-[[Category: Diphosphate-purine nucleoside kinase]]
 [[Category: Large Structures]]
-[[Category: Hino, E]]
+[[Category: Hino E]]
-[[Category: Ota, H]]
+[[Category: Ota H]]
-[[Category: Sakasegawa, S]]
+[[Category: Sakasegawa S]]
-[[Category: Tamura, T]]
+[[Category: Tamura T]]
-[[Category: Yasutake, Y]]
+[[Category: Yasutake Y]]
-[[Category: Atp binding]]
-[[Category: Kinase]]
-[[Category: Mg binding]]
-[[Category: Nucleoside binding]]
-[[Category: Rossmann fold]]
-[[Category: Transferase]]

3b1n

From Proteopedia

Revision as of 08:51, 11 October 2023

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with ADP-mizoribine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox