3gai: Difference between revisions

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{{Seed}}
[[Image:3gai.jpg|left|200px]]


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==Structure of a F112A variant PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP==
The line below this paragraph, containing "STRUCTURE_3gai", creates the "Structure Box" on the page.
<StructureSection load='3gai' size='340' side='right'caption='[[3gai]], [[Resolution|resolution]] 1.48&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'>[[3gai]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Limosilactobacillus_reuteri Limosilactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GAI 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]] 1.48&#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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
{{STRUCTURE_3gai|  PDB=3gai  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gai OCA], [https://pdbe.org/3gai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gai RCSB], [https://www.ebi.ac.uk/pdbsum/3gai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gai ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q50EJ2_LIMRT Q50EJ2_LIMRT]
== 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/ga/3gai_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3gai ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
ATP:Corrinoid adenosyltransferases (ACAs) catalyze the transfer of the adenosyl moiety from ATP to cob(I)alamin via a four-coordinate cob(II)alamin intermediate. At present, it is unknown how ACAs promote the formation of the four-coordinate corrinoid species needed for activity. The published high-resolution crystal structure of the ACA from Lactobacillus reuteri (LrPduO) in complex with ATP and cob(II)alamin shows that the environment around the alpha face of the corrin ring consists of bulky hydrophobic residues. To understand how these residues promote the generation of the four-coordinate cob(II)alamin, variants of the human-type ACA enzyme from L. reuteri (LrPduO) were kinetically and structurally characterized. These studies revealed that residue Phe112 is critical in the displacement of 5,6-dimethylbenzimidazole (DMB) from its coordination bond with the Co ion of the ring, resulting in the formation of the four-coordinate species. An F112A substitution resulted in a 80% drop in the catalytic efficiency of the enzyme. The explanation for this loss of activity was obtained from the crystal structure of the mutant protein, which showed cob(II)alamin bound in the active site with DMB coordinated to the cobalt ion. The crystal structure of an LrPduO(F112H) variant showed a DMB-off/His-on interaction between the corrinoid and the enzyme, whose catalytic efficiency was 4 orders of magnitude lower than that of the wild-type protein. The analysis of the kinetic parameters of LrPduO(F112H) suggests that the F112H substitution negatively impacts product release. Substitutions of other hydrophobic residues in the Cbl binding pocket did not result in significant defects in catalytic efficiency in vitro; however, none of the variant enzymes analyzed in this work supported AdoCbl biosynthesis in vivo.


===Structure of a F112A variant PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP===
Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme.,Mera PE, St Maurice M, Rayment I, Escalante-Semerena JC Biochemistry. 2009 Apr 14;48(14):3138-45. PMID:19236001<ref>PMID:19236001</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 19236001 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_19236001}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3GAI is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAI OCA].
[[Category: Limosilactobacillus reuteri]]
 
[[Category: Escalante-Semerena JC]]
==Reference==
[[Category: Mera PE]]
<ref group="xtra">PMID:19236001</ref><references group="xtra"/>
[[Category: Rayment I]]
[[Category: Lactobacillus reuteri]]
[[Category: St Maurice M]]
[[Category: Escalante-Semerena, J C.]]
[[Category: Maurice, M St.]]
[[Category: Mera, P E.]]
[[Category: Rayment, I.]]
[[Category: Transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  8 09:25:57 2009''
Retrieved from "https://proteopedia.org/3gai"