3dh7: Difference between revisions

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==Structure of T. thermophilus IDI-2 in complex with PPi==
==Structure of T. thermophilus IDI-2 in complex with PPi==
<StructureSection load='3dh7' size='340' side='right' caption='[[3dh7]], [[Resolution|resolution]] 2.97&Aring;' scene=''>
<StructureSection load='3dh7' size='340' side='right'caption='[[3dh7]], [[Resolution|resolution]] 2.97&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3dh7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DH7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DH7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3dh7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DH7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DH7 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.97&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHB110 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dh7 OCA], [http://pdbe.org/3dh7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dh7 RCSB], [http://www.ebi.ac.uk/pdbsum/3dh7 PDBsum]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dh7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dh7 OCA], [https://pdbe.org/3dh7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dh7 RCSB], [https://www.ebi.ac.uk/pdbsum/3dh7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dh7 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/Q53W52_THET8 Q53W52_THET8]] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).[HAMAP-Rule:MF_00354]  
[https://www.uniprot.org/uniprot/Q53W52_THET8 Q53W52_THET8] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).[HAMAP-Rule:MF_00354]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dh/3dh7_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dh/3dh7_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 19: Line 20:
</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=3dh7 ConSurf].
</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=3dh7 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The N-terminal region is stabilized in the crystal structure of Thermus thermophilus type 2 isopentenyl diphosphate isomerase in complex with inorganic pyrophosphate, providing new insights about the active site and the catalytic mechanism of the enzyme. The PP i moiety is located near the conserved residues, H10, R97, H152, Q157, E158, and W219, and the flavin cofactor. The putative active site of isopentenyl diphosphate isomerase 2 provides interactions for stabilizing a carbocationic intermediate similar to those that stabilize the intermediate in the well-established protonation-deprotonation mechanism of isopentenyl diphosphate isomerase 1.
Crystal structure of type 2 isopentenyl diphosphate isomerase from Thermus thermophilus in complex with inorganic pyrophosphate.,de Ruyck J, Pouyez J, Rothman SC, Poulter D, Wouters J Biochemistry. 2008 Sep 2;47(35):9051-3. Epub 2008 Aug 12. PMID:18693754<ref>PMID:18693754</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3dh7" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Thet8]]
[[Category: Large Structures]]
[[Category: Ruyck, J de]]
[[Category: Thermus thermophilus HB8]]
[[Category: Wouters, J]]
[[Category: Wouters J]]
[[Category: Complex]]
[[Category: De Ruyck J]]
[[Category: Idi]]
[[Category: Isomerase]]

Latest revision as of 11:24, 20 March 2024

Structure of T. thermophilus IDI-2 in complex with PPiStructure of T. thermophilus IDI-2 in complex with PPi

Structural highlights

3dh7 is a 4 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.97Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q53W52_THET8 Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP).[HAMAP-Rule:MF_00354]

Evolutionary Conservation

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

See Also

3dh7, resolution 2.97Å

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