Proteopedia

1q54: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1q54.jpg|left|200px]]


{{Structure
==STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP==
|PDB= 1q54 |SIZE=350|CAPTION= <scene name='initialview01'>1q54</scene>, resolution 1.93&Aring;
<StructureSection load='1q54' size='340' side='right'caption='[[1q54]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=BHI:4-BROMO-3-HYDROXY-3-METHYL+BUTYL+DIPHOSPHATE'>BHI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>
<table><tr><td colspan='2'>[[1q54]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1n2u 1n2u]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q54 FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Isopentenyl-diphosphate_Delta-isomerase Isopentenyl-diphosphate Delta-isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.2 5.3.3.2] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.93&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BHI:4-BROMO-3-HYDROXY-3-METHYL+BUTYL+DIPHOSPHATE'>BHI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q54 OCA], [https://pdbe.org/1q54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q54 RCSB], [https://www.ebi.ac.uk/pdbsum/1q54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q54 ProSAT]</span></td></tr>
|RELATEDENTRY=[[1hzt|1HZT]], [[1hx3|1HX3]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q54 OCA], [http://www.ebi.ac.uk/pdbsum/1q54 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q54 RCSB]</span>
== 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/q5/1q54_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=1q54 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have obtained the three-dimensional X-ray crystallographic structure of a C67A mutant Escherichia coli isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase (EC 5.3.3.2) complexed with the bromohydrin of isopentenylpyrophosphate, at 1.93 A resolution. The overall backbone fold is very similar to that obtained previously for the wild-type enzyme in the presence of a divalent metal cation (Mn2+ or Mg2+). However, in the new structure, there are two metal binding sites, not just one. The first metal binding site is occupied by Mn2+, coordinated to three histidine and two glutamate residues, while the second is occupied by Mg2+, coordinated to two bromohydrin-ligand phosphate oxygens, the carbonyl oxygen of A67, a carboxyl oxygen of E87, and two water molecules. The C3 hydroxyl group of the bromohydrin inhibitor is involved in a short hydrogen bond to the carboxyl group of E116, one of the two Mn-bound glutamates. The structure obtained is consistent with a mechanism of action of the enzyme in which the carboxyl group of E116 protonates the double bond in isopentenylpyrophosphate, forming a carbocation, followed by removal of a C2 proton by the thiolate of C67, in the wild-type enzyme. The inhibition of the enzyme by a wide variety of other potent inhibitors is also readily explained on the basis of the bromohydrin inhibitor structure.


'''STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP'''
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase.,Wouters J, Oudjama Y, Ghosh S, Stalon V, Droogmans L, Oldfield E J Am Chem Soc. 2003 Mar 19;125(11):3198-9. PMID:12630859<ref>PMID:12630859</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1q54" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
We have obtained the three-dimensional X-ray crystallographic structure of a C67A mutant Escherichia coli isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase (EC 5.3.3.2) complexed with the bromohydrin of isopentenylpyrophosphate, at 1.93 A resolution. The overall backbone fold is very similar to that obtained previously for the wild-type enzyme in the presence of a divalent metal cation (Mn2+ or Mg2+). However, in the new structure, there are two metal binding sites, not just one. The first metal binding site is occupied by Mn2+, coordinated to three histidine and two glutamate residues, while the second is occupied by Mg2+, coordinated to two bromohydrin-ligand phosphate oxygens, the carbonyl oxygen of A67, a carboxyl oxygen of E87, and two water molecules. The C3 hydroxyl group of the bromohydrin inhibitor is involved in a short hydrogen bond to the carboxyl group of E116, one of the two Mn-bound glutamates. The structure obtained is consistent with a mechanism of action of the enzyme in which the carboxyl group of E116 protonates the double bond in isopentenylpyrophosphate, forming a carbocation, followed by removal of a C2 proton by the thiolate of C67, in the wild-type enzyme. The inhibition of the enzyme by a wide variety of other potent inhibitors is also readily explained on the basis of the bromohydrin inhibitor structure.
*[[Isopentenyl-diphosphate delta-isomerase|Isopentenyl-diphosphate delta-isomerase]]
 
== References ==
==About this Structure==
<references/>
1Q54 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry 1N2U. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q54 OCA].
__TOC__
 
</StructureSection>
==Reference==
Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase., Wouters J, Oudjama Y, Ghosh S, Stalon V, Droogmans L, Oldfield E, J Am Chem Soc. 2003 Mar 19;125(11):3198-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12630859 12630859]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Isopentenyl-diphosphate Delta-isomerase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Droogmans L]]
[[Category: Droogmans, L.]]
[[Category: Ghosh S]]
[[Category: Ghosh, S.]]
[[Category: Oudjama Y]]
[[Category: Oudjama, Y.]]
[[Category: Stalon V]]
[[Category: Stalon, V.]]
[[Category: Wouters J]]
[[Category: Wouters, J.]]
[[Category: complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:08:55 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/1q54"