We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

3aqb

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 12:35, 5 August 2016

M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium

Structural highlights

3aqb is a 4 chain structure with sequence from "bacteridium_luteum"_schroeter_1872 "bacteridium luteum" schroeter 1872. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3aqc
Gene:	hexs-a ("Bacteridium luteum" Schroeter 1872), hexs-b ("Bacteridium luteum" Schroeter 1872)
Activity:	Transferase, with EC number and 2.5.1.83 2.5.1.82 and 2.5.1.83
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2] ^[3] [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.^[4] ^[5] ^[6]

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^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nagaki M, Kimura K, Kimura H, Maki Y, Goto E, Nishino T, Koyama T. Artificial substrates of medium-chain elongating enzymes, hexaprenyl- and heptaprenyl diphosphate synthases. Bioorg Med Chem Lett. 2001 Aug 20;11(16):2157-9. PMID:11514159
↑ Fujii H, Koyama T, Ogura K. Hexaprenyl pyrophosphate synthetase from Micrococcus luteus B-P 26. Separation of two essential components. J Biol Chem. 1982 Dec 25;257(24):14610-2. PMID:7174655
↑ Shimizu N, Koyama T, Ogura K. Molecular cloning, expression, and characterization of the genes encoding the two essential protein components of Micrococcus luteus B-P 26 hexaprenyl diphosphate synthase. J Bacteriol. 1998 Mar;180(6):1578-81. PMID:9515931
↑ Nagaki M, Kimura K, Kimura H, Maki Y, Goto E, Nishino T, Koyama T. Artificial substrates of medium-chain elongating enzymes, hexaprenyl- and heptaprenyl diphosphate synthases. Bioorg Med Chem Lett. 2001 Aug 20;11(16):2157-9. PMID:11514159
↑ Fujii H, Koyama T, Ogura K. Hexaprenyl pyrophosphate synthetase from Micrococcus luteus B-P 26. Separation of two essential components. J Biol Chem. 1982 Dec 25;257(24):14610-2. PMID:7174655
↑ Shimizu N, Koyama T, Ogura K. Molecular cloning, expression, and characterization of the genes encoding the two essential protein components of Micrococcus luteus B-P 26 hexaprenyl diphosphate synthase. J Bacteriol. 1998 Mar;180(6):1578-81. PMID:9515931
↑ Sasaki D, Fujihashi M, Okuyama N, Kobayashi Y, Noike M, Koyama T, Miki K. 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. J Biol Chem. 2011 Feb 4;286(5):3729-40. Epub 2010 Nov 9. PMID:21068379 doi:10.1074/jbc.M110.147991

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3aqb"

@@ Line 1: / Line 1: @@
 ==M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium==
 <StructureSection load='3aqb' size='340' side='right' caption='[[3aqb]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3aqb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Micrococcus_luteus Micrococcus luteus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AQB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3aqb]] 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=3AQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AQB FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3aqc|3aqc]]</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 Micrococcus luteus]), hexs-b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1270 Micrococcus luteus])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trans-pentaprenyltranstransferase Trans-pentaprenyltranstransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.33 2.5.1.33] </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=3aqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aqb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3aqb RCSB], [http://www.ebi.ac.uk/pdbsum/3aqb PDBsum]</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=3aqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aqb OCA], [http://pdbe.org/3aqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3aqb RCSB], [http://www.ebi.ac.uk/pdbsum/3aqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3aqb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/O66127_MICLU O66127_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/O66129_MICLU O66129_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/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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3aqb" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Micrococcus luteus]]
+[[Category: Bacteridium luteum schroeter 1872]]
-[[Category: Trans-pentaprenyltranstransferase]]
+[[Category: Transferase]]
 [[Category: Fujihashi, M]]
 [[Category: Kobayashi, Y]]
@@ Line 33: / Line 35: @@
 [[Category: Sasaki, D]]
 [[Category: Prenyltransferase]]
-[[Category: Transferase]]

3aqb

From Proteopedia

Revision as of 12:35, 5 August 2016

M. luteus B-P 26 heterodimeric hexaprenyl diphosphate synthase in complex with magnesium

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox