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2h39

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Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose

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-[[Image:2h39.gif|left|200px]]<br /><applet load="2h39" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2h39, resolution 2.230&Aring;" />
-'''Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose'''<br />
-==Overview==
+==Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose==
-The X-ray crystal structure of the At5g18200.1 protein has been determined, to a nominal resolution of 2.30 A. The structure has a histidine triad, (HIT)-like fold containing two distinct HIT-like motifs. The sequence of, At5g18200.1 indicates a distant family relationship to the Escherichia, coli galactose-1-P uridylyltransferase (GalT): the determined structure of, the At5g18200.1 protein confirms this relationship. The At5g18200.1, protein does not demonstrate GalT activity but instead catalyzes adenylyl, transfer in the reaction of ADP-glucose with various phosphates. The best, acceptor among those evaluated is phosphate itself; thus, the At5g18200.1, enzyme appears to be an ADP-glucose phosphorylase. The enzyme catalyzes, the exchange of (14)C between ADP-[(14)C]glucose and glucose-1-P in the, absence of phosphate. The steady state kinetics of exchange follows the, ping-pong bi-bi kinetic mechanism, with a k(cat) of 4.1 s(-)(1) and K(m), values of 1.4 and 83 microM for ADP-[(14)C]glucose and glucose-1-P, respectively, at pH 8.5 and 25 degrees C. The overall reaction of, ADP-glucose with phosphate to produce ADP and glucose-1-P follows, ping-pong bi-bi steady state kinetics, with a k(cat) of 2.7 s(-)(1) and, K(m) values of 6.9 and 90 microM for ADP-glucose and phosphate, respectively, at pH 8.5 and 25 degrees C. The kinetics are consistent with, a double-displacement mechanism that involves a covalent adenylyl-enzyme, intermediate. The X-ray crystal structure of this intermediate was, determined to 1.83 A resolution and shows the AMP group bonded to, His(186). The value of K(eq) in the direction of ADP and glucose-1-P, formation is 5.0 at pH 7.0 and 25 degrees C in the absence of a divalent, metal ion, and it is 40 in the presence of 1 mM MgCl(2).
+<StructureSection load='2h39' size='340' side='right'caption='[[2h39]], [[Resolution|resolution]] 2.23&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2h39]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2gdk 2gdk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H39 FirstGlance]. <br>
-H39 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with ZN, CL and ADQ as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 2GDK. Active as [http://en.wikipedia.org/wiki/UDP-glucose--hexose-1-phosphate_uridylyltransferase UDP-glucose--hexose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.12 2.7.7.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2H39 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.23&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADQ:ADENOSINE-5-DIPHOSPHATE-GLUCOSE'>ADQ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2h39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h39 OCA], [https://pdbe.org/2h39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h39 RCSB], [https://www.ebi.ac.uk/pdbsum/2h39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h39 ProSAT]</span></td></tr>
-Structure and mechanism of an ADP-glucose phosphorylase from Arabidopsis thaliana., McCoy JG, Arabshahi A, Bitto E, Bingman CA, Ruzicka FJ, Frey PA, Phillips GN Jr, Biochemistry. 2006 Mar 14;45(10):3154-62. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16519510 16519510]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AGLUP_ARATH AGLUP_ARATH] Catalyzes the conversion of ADP-glucose and inorganic phosphate (Pi) into glucose-1-phosphate and ADP. Does not possess galactose-1-phosphate uridylyltransferase activity.<ref>PMID:16519510</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h3/2h39_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2h39 ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: UDP-glucose--hexose-1-phosphate uridylyltransferase]]
+[[Category: Bingman CA]]
-[[Category: Bingman, C.A.]]
+[[Category: Bitto E]]
-[[Category: Bitto, E.]]
+[[Category: McCoy JG]]
-[[Category: CESG, Center.for.Eukaryotic.Structural.Genomics.]]
+[[Category: Phillips Jr GN]]
-[[Category: Jr., G.N.Phillips.]]
+[[Category: Wesenberg GE]]
-[[Category: McCoy, J.G.]]
-[[Category: Wesenberg, G.E.]]
-[[Category: ADQ]]
-[[Category: CL]]
-[[Category: ZN]]
-[[Category: adp-glucose]]
-[[Category: at5g18200]]
-[[Category: center for eukaryotic structural genomics]]
-[[Category: cesg]]
-[[Category: galt-like]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: structural genomics functional follow-up study]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:31:38 2007''

2h39

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Crystal Structure of an ADP-Glucose Phosphorylase from Arabidopsis thaliana with bound ADP-Glucose

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Evolutionary Conservation

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