2b2k

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2b2k" [edit=sysop:move=sysop])
Current revision (07:46, 23 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2b2k.png|left|200px]]
 
-
<!--
+
==structure of Y104F IDI-1 mutant in complex with EIPP==
-
The line below this paragraph, containing "STRUCTURE_2b2k", creates the "Structure Box" on the page.
+
<StructureSection load='2b2k' size='340' side='right'caption='[[2b2k]], [[Resolution|resolution]] 1.97&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'>[[2b2k]] is a 2 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=2B2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B2K 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]] 1.97&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EIP:4-HYDROXY-3-METHYL+BUTYL+DIPHOSPHATE'>EIP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
{{STRUCTURE_2b2k| PDB=2b2k | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b2k OCA], [https://pdbe.org/2b2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b2k RCSB], [https://www.ebi.ac.uk/pdbsum/2b2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b2k ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/IDI_ECOLI IDI_ECOLI] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP).<ref>PMID:10099534</ref> <ref>PMID:9603997</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/b2/2b2k_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=2b2k ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate isomerase is a key enzyme in the biosynthesis of isoprenoids. The mechanism of the isomerization reaction involves protonation of the unactivated carbon-carbon double bond in the substrate, but identity of the acidic moiety providing the proton is still not clear. Multiple sequence alignments and geometrical features observed in crystal structures of complexes with IPP isomerase suggest that Tyr-104 could play an important role during catalysis. A series of mutants was constructed by directed mutagenesis and characterized by enzymology. Crystallographic and thermal denaturation data for Y104A and Y104F mutants were obtained. Those data demonstrate the importance of residue Tyr-104 for proper folding of Escherichia coli type I IPP isomerase.
-
===structure of Y104F IDI-1 mutant in complex with EIPP===
+
Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography.,de Ruyck J, Durisotti V, Oudjama Y, Wouters J J Biol Chem. 2006 Jun 30;281(26):17864-9. Epub 2006 Apr 15. PMID:16617181<ref>PMID:16617181</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2b2k" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_16617181}}, adds the Publication Abstract to the page
+
*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 16617181 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_16617181}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
[[2b2k]] is a 2 chain structure with 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=2B2K OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:016617181</ref><references group="xtra"/>
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Isopentenyl-diphosphate Delta-isomerase]]
+
[[Category: Large Structures]]
-
[[Category: Wouters, J.]]
+
[[Category: Wouters J]]
-
[[Category: Complex]]
+
-
[[Category: Isomerase]]
+

Current revision

structure of Y104F IDI-1 mutant in complex with EIPP

PDB ID 2b2k

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2b2k"
Personal tools