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| | <StructureSection load='4n02' size='340' side='right'caption='[[4n02]], [[Resolution|resolution]] 1.40Å' scene=''> | | <StructureSection load='4n02' size='340' side='right'caption='[[4n02]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4n02]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N02 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4n02]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_CGSP14 Streptococcus pneumoniae CGSP14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N02 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FNR:1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL'>FNR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4n02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n02 OCA], [https://pdbe.org/4n02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n02 RCSB], [https://www.ebi.ac.uk/pdbsum/4n02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n02 ProSAT]</span></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=4n02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n02 OCA], [http://pdbe.org/4n02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n02 RCSB], [http://www.ebi.ac.uk/pdbsum/4n02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n02 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/IDI2_STRPS IDI2_STRPS]] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity). | + | [https://www.uniprot.org/uniprot/IDI2_STRPS IDI2_STRPS] Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Isopentenyl-diphosphate Delta-isomerase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Streptococcus pneumoniae]] | + | [[Category: Streptococcus pneumoniae CGSP14]] |
| - | [[Category: Poulter, C D]] | + | [[Category: Poulter CD]] |
| - | [[Category: Ruyck, J de]]
| + | [[Category: Schubert HL]] |
| - | [[Category: Schubert, H L]] | + | [[Category: De Ruyck J]] |
| - | [[Category: Isomerase]] | + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
IDI2_STRPS Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its allylic isomer, dimethylallyl diphosphate (DMAPP) (By similarity).
Publication Abstract from PubMed
Isopentenyl diphosphate isomerase (IDI) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. Type 1 IDI (IDI-1) is a metalloprotein that is found in eukaryotes, whereas the type 2 isoform (IDI-2) is a flavoenzyme found in bacteria that is completely absent from human. IDI-2 from the pathogenic bacterium Streptococcus pneumoniae was recombinantly expressed in Escherichia coli. Steady-state kinetic studies of the enzyme indicated that FMNH2 (KM =0.3 muM) bound before isopentenyl diphosphate (KM =40 muM) in an ordered binding mechanism. An X-ray crystal structure at 1.4 A resolution was obtained for the holoenzyme in the closed conformation with a reduced flavin cofactor and two sulfate ions in the active site. These results helped to further approach the enzymatic mechanism of IDI-2 and, thus, open new possibilities for the rational design of antibacterial compounds against sequence-similar and structure-related pathogens such as Enterococcus faecalis or Staphylococcus aureus.
Determination of Kinetics and the Crystal Structure of a Novel Type 2 Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase from Streptococcus pneumoniae.,de Ruyck J, Janczak MW, Neti SS, Rothman SC, Schubert HL, Cornish RM, Matagne A, Wouters J, Poulter CD Chembiochem. 2014 Jul 7;15(10):1452-8. doi: 10.1002/cbic.201402046. Epub 2014 Jun, 6. PMID:24910111[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ de Ruyck J, Janczak MW, Neti SS, Rothman SC, Schubert HL, Cornish RM, Matagne A, Wouters J, Poulter CD. Determination of Kinetics and the Crystal Structure of a Novel Type 2 Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase from Streptococcus pneumoniae. Chembiochem. 2014 Jul 7;15(10):1452-8. doi: 10.1002/cbic.201402046. Epub 2014 Jun, 6. PMID:24910111 doi:http://dx.doi.org/10.1002/cbic.201402046
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