3aqc: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
 ==M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium and FPP analogue==
-<StructureSection load='3aqc' size='340' side='right' caption='[[3aqc]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
+<StructureSection load='3aqc' size='340' side='right'caption='[[3aqc]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3aqc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteridium_luteum"_schroeter_1872 "bacteridium luteum" schroeter 1872]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AQC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AQC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3aqc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Micrococcus_luteus Micrococcus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AQC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DE:(2E,6E)-7,11-DIMETHYLDODECA-2,6,10-TRIEN-1-YL+TRIHYDROGEN+DIPHOSPHATE'>2DE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.61&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3aqb|3aqb]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DE:(2E,6E)-7,11-DIMETHYLDODECA-2,6,10-TRIEN-1-YL+TRIHYDROGEN+DIPHOSPHATE'>2DE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hexs-a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1270 "Bacteridium luteum" Schroeter 1872]), hexs-b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1270 "Bacteridium luteum" Schroeter 1872])</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=3aqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aqc OCA], [https://pdbe.org/3aqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aqc RCSB], [https://www.ebi.ac.uk/pdbsum/3aqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aqc ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.82 and 2.5.1.83 2.5.1.82 and 2.5.1.83] </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=3aqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aqc OCA], [http://pdbe.org/3aqc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3aqc RCSB], [http://www.ebi.ac.uk/pdbsum/3aqc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3aqc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HEXA_MICLU HEXA_MICLU]] Catalyzes the condensation of three molecules of isopentenyl diphosphate with farnesyl diphosphate (FPP) to yield (all-E)-hexaprenyl diphosphate (HexPP; C30), the precursor of the prenyl side chain of menaquinone-6. Large subunit Hexs-B catalyzes the condensation reaction and the final product chain length is cooperatively regulated by both the Hexs-A and Hexs-B subunits using the whole size of the hydrophobic cleft as a ruler.<ref>PMID:11514159</ref> <ref>PMID:7174655</ref> <ref>PMID:9515931</ref>  [[http://www.uniprot.org/uniprot/HEXB_MICLU HEXB_MICLU]] Catalyzes the condensation of three molecules of isopentenyl diphosphate with farnesyl diphosphate (FPP) to yield (all-E)-hexaprenyl diphosphate (HexPP; C30), the precursor of the prenyl side chain of menaquinone-6. Large subunit Hexs-B catalyzes the condensation reaction and the final product chain length is cooperatively regulated by both the Hexs-A and Hexs-B subunits using the whole size of the hydrophobic cleft as a ruler.<ref>PMID:11514159</ref> <ref>PMID:7174655</ref> <ref>PMID:9515931</ref>
+[https://www.uniprot.org/uniprot/HEXA_MICLU HEXA_MICLU] Catalyzes the condensation of three molecules of isopentenyl diphosphate with farnesyl diphosphate (FPP) to yield (all-E)-hexaprenyl diphosphate (HexPP; C30), the precursor of the prenyl side chain of menaquinone-6. Large subunit Hexs-B catalyzes the condensation reaction and the final product chain length is cooperatively regulated by both the Hexs-A and Hexs-B subunits using the whole size of the hydrophobic cleft as a ruler.<ref>PMID:11514159</ref> <ref>PMID:7174655</ref> <ref>PMID:9515931</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 (Ml-HexPPs) is a heterooligomeric type trans-prenyltransferase catalyzing consecutive head-to-tail condensations of three molecules of isopentenyl diphosphates (C(5)) on a farnesyl diphosphate (FPP; C(15)) to form an (all-E) hexaprenyl diphosphate (HexPP; C(30)). Ml-HexPPs is known to function as a heterodimer of two different subunits, small and large subunits called HexA and HexB, respectively. Compared with homooligomeric trans-prenyltransferases, the molecular mechanism of heterooligomeric trans-prenyltransferases is not yet clearly understood, particularly with respect to the role of the small subunits lacking the catalytic motifs conserved in most known trans-prenyltransferases. We have determined the crystal structure of Ml-HexPPs both in the substrate-free form and in complex with 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate ammonium salt (3-DesMe-FPP), an analog of FPP. The structure of HexB is composed of mostly antiparallel alpha-helices joined by connecting loops. Two aspartate-rich motifs (designated the first and second aspartate-rich motifs) and the other characteristic motifs in HexB are located around the diphosphate part of 3-DesMe-FPP. Despite the very low amino acid sequence identity and the distinct polypeptide chain lengths between HexA and HexB, the structure of HexA is quite similar to that of HexB. The aliphatic tail of 3-DesMe-FPP is accommodated in a large hydrophobic cleft starting from HexB and penetrating to the inside of HexA. These structural features suggest that HexB catalyzes the condensation reactions and that HexA is directly involved in the product chain length control in cooperation with HexB.
-Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation.,Sasaki D, Fujihashi M, Okuyama N, Kobayashi Y, Noike M, Koyama T, Miki K J Biol Chem. 2011 Feb 4;286(5):3729-40. Epub 2010 Nov 9. PMID:21068379<ref>PMID:21068379</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3aqc" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteridium luteum schroeter 1872]]
+[[Category: Large Structures]]
-[[Category: Transferase]]
+[[Category: Micrococcus luteus]]
-[[Category: Fujihashi, M]]
+[[Category: Fujihashi M]]
-[[Category: Kobayashi, Y]]
+[[Category: Kobayashi Y]]
-[[Category: Koyama, T]]
+[[Category: Koyama T]]
-[[Category: Miki, K]]
+[[Category: Miki K]]
-[[Category: Noike, M]]
+[[Category: Noike M]]
-[[Category: Okuyama, N]]
+[[Category: Okuyama N]]
-[[Category: Sasaki, D]]
+[[Category: Sasaki D]]
-[[Category: Prenyltransferase]]