2ate: Difference between revisions

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


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==Structure of the complex of PurE with NitroAIR==
The line below this paragraph, containing "STRUCTURE_2ate", creates the "Structure Box" on the page.
<StructureSection load='2ate' size='340' side='right'caption='[[2ate]], [[Resolution|resolution]] 1.80&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'>[[2ate]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ATE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ATE FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NIA:((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL+DIHYDROGEN+PHOSPHATE'>NIA</scene></td></tr>
{{STRUCTURE_2ate|  PDB=2ate  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ate FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ate OCA], [https://pdbe.org/2ate PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ate RCSB], [https://www.ebi.ac.uk/pdbsum/2ate PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ate ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PURE_ECOLI PURE_ECOLI] Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR).
== 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/at/2ate_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=2ate ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
N5-Carboxyaminoimidazole ribonucleotide mutase (N5-CAIR mutase or PurE) from Escherichia coli catalyzes the reversible interconversion of N5-CAIR to carboxyaminoimidazole ribonucleotide (CAIR) with direct CO2 transfer. Site-directed mutagenesis, a pH-rate profile, DFT calculations, and X-ray crystallography together provide new insight into the mechanism of this unusual transformation. These studies suggest that a conserved, protonated histidine (His45) plays an essential role in catalysis. The importance of proton transfers is supported by DFT calculations on CAIR and N5-CAIR analogues in which the ribose 5'-phosphate is replaced with a methyl group. The calculations suggest that the nonaromatic tautomer of CAIR (isoCAIR) is only 3.1 kcal/mol higher in energy than its aromatic counterpart, implicating this species as a potential intermediate in the PurE-catalyzed reaction. A structure of wild-type PurE cocrystallized with 4-nitroaminoimidazole ribonucleotide (NO2-AIR, a CAIR analogue) and structures of H45N and H45Q PurEs soaked with CAIR have been determined and provide the first insight into the binding of an intact PurE substrate. A comparison of 19 available structures of PurE and PurE mutants in apo and nucleotide-bound forms reveals a common, buried carboxylate or CO2 binding site for CAIR and N5-CAIR in a hydrophobic pocket in which the carboxylate or CO2 interacts with backbone amides. This work has led to a mechanistic proposal in which the carboxylate orients the substrate for proton transfer from His45 to N5-CAIR to form an enzyme-bound aminoimidazole ribonucleotide (AIR) and CO2 intermediate. Subsequent movement of the aminoimidazole moiety of AIR reorients it for addition of CO2 at C4 to generate isoCAIR. His45 is now in a position to remove a C4 proton to produce CAIR.


'''Structure of the complex of PurE with NitroAIR'''
N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis.,Hoskins AA, Morar M, Kappock TJ, Mathews II, Zaugg JB, Barder TE, Peng P, Okamoto A, Ealick SE, Stubbe J Biochemistry. 2007 Mar 13;46(10):2842-55. Epub 2007 Feb 14. PMID:17298082<ref>PMID:17298082</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ate" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Structural studies, sequence alignments, and biochemistry have provided new insights into the evolution of the purine biosynthetic pathway. The importance of chemistry, the binding of ribose 5-phosphate (common to all purine biosynthetic intermediates), and transient protein-protein interactions in channeling of chemically unstable intermediates have all been examined in the past few years.
*[[Phosphoribosylaminoimidazole carboxylase 3D structures|Phosphoribosylaminoimidazole carboxylase 3D structures]]
 
== References ==
==About this Structure==
<references/>
2ATE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ATE OCA].
__TOC__
 
</StructureSection>
==Reference==
Modular evolution of the purine biosynthetic pathway., Kappock TJ, Ealick SE, Stubbe J, Curr Opin Chem Biol. 2000 Oct;4(5):567-72. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11006546 11006546]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Phosphoribosylaminoimidazole carboxylase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Ealick SE]]
[[Category: Ealick, S E.]]
[[Category: Hoskins AA]]
[[Category: Hoskins, A A.]]
[[Category: Kappock TJ]]
[[Category: Kappock, T J.]]
[[Category: Mathews II]]
[[Category: Mathews, I I.]]
[[Category: Okamoto A]]
[[Category: Okamoto, A.]]
[[Category: Peng P]]
[[Category: Peng, P.]]
[[Category: Stubbe J]]
[[Category: Stubbe, J.]]
[[Category: Zaugg JB]]
[[Category: Zaugg, J B.]]
[[Category: Nitroair complex]]
[[Category: Pure]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 19:27:09 2008''
Retrieved from "https://proteopedia.org/2ate"