2pa4: Difference between revisions

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New page: left|200px<br /><applet load="2pa4" size="350" color="white" frame="true" align="right" spinBox="true" caption="2pa4, resolution 2.0Å" /> '''Crystal structure of ...
 
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[[Image:2pa4.gif|left|200px]]<br /><applet load="2pa4" size="350" color="white" frame="true" align="right" spinBox="true"
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'''Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose'''<br />


==Overview==
==Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose==
Glucose-1-phosphate uridylyltransferase, or UGPase, catalyzes the, production of UDP-glucose from glucose-1-phosphate and UTP. Because of the, biological role of UDP-glucose in glycogen synthesis and in the formation, of glycolipids, glycoproteins, and proteoglycans, the enzyme is widespread, in nature. Recently this laboratory reported the three-dimensional, structure of UGPase from Escherichia coli. While the initial X-ray, analysis revealed the overall fold of the enzyme, details concerning its, active site geometry were limited because crystals of the protein, complexed with either substrates or products could never be obtained. In, an effort to more fully investigate the active site geometry of the, enzyme, UGPase from Corynebacterium glutamicum was subsequently cloned and, purified. Here we report the X-ray structure of UGPase crystallized in the, presence of both magnesium and UDP-glucose. Residues involved in anchoring, the ligand to the active site include the polypeptide chain backbone atoms, of Ala 20, Gly 21, Gly 117, Gly 180, and Ala 214, and the side chains of, Glu 36, Gln 112, Asp 143, Glu 201, and Lys 202. Two magnesium ions are, observed coordinated to the UDP-glucose. An alpha- and a beta-phosphoryl, oxygen, three waters, and the side chain of Asp 142 ligate the first, magnesium, whereas the second ion is coordinated by an alpha-phosphoryl, oxygen and five waters. The position of the first magnesium is conserved, in both the glucose-1-phosphate thymidylyltransferases and the, cytidylyltransferases. The structure presented here provides further, support for the role of the conserved magnesium ion in the catalytic, mechanisms of the sugar-1-phosphate nucleotidylyltransferases.
<StructureSection load='2pa4' size='340' side='right'caption='[[2pa4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2pa4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PA4 FirstGlance]. <br>
2PA4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=GUD:'>GUD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/UTP--glucose-1-phosphate_uridylyltransferase UTP--glucose-1-phosphate uridylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.9 2.7.7.9] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 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&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</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=2pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pa4 OCA], [https://pdbe.org/2pa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pa4 RCSB], [https://www.ebi.ac.uk/pdbsum/2pa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pa4 ProSAT]</span></td></tr>
Active site geometry of glucose-1-phosphate uridylyltransferase., Thoden JB, Holden HM, Protein Sci. 2007 Jul;16(7):1379-88. Epub 2007 Jun 13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17567737 17567737]
</table>
[[Category: Corynebacterium glutamicum]]
== Evolutionary Conservation ==
[[Category: Single protein]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
Check<jmol>
[[Category: Holden, H.M.]]
  <jmolCheckbox>
[[Category: Thoden, J.B.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pa/2pa4_consurf.spt"</scriptWhenChecked>
[[Category: GUD]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: MG]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: metabolism]]
  </jmolCheckbox>
[[Category: nucleotidyltransferase]]
</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=2pa4 ConSurf].
[[Category: phosphorylase]]
<div style="clear:both"></div>
 
__TOC__
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:50:09 2008''
</StructureSection>
[[Category: Corynebacterium glutamicum ATCC 13032]]
[[Category: Large Structures]]
[[Category: Holden HM]]
[[Category: Thoden JB]]

Latest revision as of 12:08, 21 February 2024

Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucoseCrystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose

Structural highlights

2pa4 is a 4 chain structure with sequence from Corynebacterium glutamicum ATCC 13032. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

2pa4, resolution 2.00Å

Drag the structure with the mouse to rotate

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