4n02
From Proteopedia
(Difference between revisions)
| Line 4: | Line 4: | ||
== Structural highlights == | == Structural highlights == | ||
<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> | <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" 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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</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='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'>[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> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[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). | [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;"> | ||
| - | == 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<ref>PMID:24910111</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4n02" 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> | ||
Current revision
Type 2 IDI from S. pneumoniae
| |||||||||||
