2pa4: Difference between revisions

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[[Image:2pa4.gif|left|200px]]


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==Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose==
The line below this paragraph, containing "STRUCTURE_2pa4", creates the "Structure Box" on the page.
<StructureSection load='2pa4' size='340' side='right'caption='[[2pa4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
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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&#8491;</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
{{STRUCTURE_2pa4|  PDB=2pa4  |  SCENE= }}
<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>
 
</table>
'''Crystal structure of UDP-glucose pyrophosphorylase from Corynebacteria glutamicum in complex with magnesium and UDP-glucose'''
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
==Overview==
  <jmolCheckbox>
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.
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pa/2pa4_consurf.spt"</scriptWhenChecked>
 
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
==About this Structure==
    <text>to colour the structure by Evolutionary Conservation</text>
2PA4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PA4 OCA].  
  </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=2pa4 ConSurf].
==Reference==
<div style="clear:both"></div>
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://www.ncbi.nlm.nih.gov/pubmed/17567737 17567737]
__TOC__
[[Category: Corynebacterium glutamicum]]
</StructureSection>
[[Category: Single protein]]
[[Category: Corynebacterium glutamicum ATCC 13032]]
[[Category: UTP--glucose-1-phosphate uridylyltransferase]]
[[Category: Large Structures]]
[[Category: Holden, H M.]]
[[Category: Holden HM]]
[[Category: Thoden, J B.]]
[[Category: Thoden JB]]
[[Category: Metabolism]]
[[Category: Nucleotidyltransferase]]
[[Category: Phosphorylase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 12:42:15 2008''

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

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