This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3atr

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius co-crystallized with its ligand

Structural highlights

3atr is a 1 chain structure with sequence from Sulfolobus acidocaldarius. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GGR_SULAC Is involved in the reduction of 2,3-digeranylgeranylglycerophospholipids (unsaturated archaeols) into 2,3-diphytanylglycerophospholipids (saturated archaeols) in the biosynthesis of archaeal membrane lipids. Catalyzes the formation of archaetidic acid (2,3-di-O-phytanyl-sn-glyceryl phosphate) from 2,3-di-O-geranylgeranylglyceryl phosphate (DGGGP) via the hydrogenation of each double bond of the isoprenoid chains. Is not active with NADPH or NADH as an electron donor; the physiological reducing agent is unknown. Is also active on the more upstream precursors of membrane lipid biosynthesis, catalyzing the complete reduction of 3-O-geranylgeranylglyceryl phosphate (GGGP) to 3-O-phytanylglyceryl phosphate, and the partial reduction of geranylgeranyl diphosphate (GGPP) to phytyl diphosphate, thus reducing three of four GGPP double bonds and preserving the allylic double bond (at position 2). This reaction product is a reactive prenyl donor, which can be used as a substrate by archaeal prenyltransferases such as GGGP synthases.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The crystal structure of geranylgeranyl reductase (GGR) from Sulfolobus acidocaldarius was determined in order to elucidate the molecular mechanism of the catalytic reaction. The enzyme is a flavoprotein and is involved in saturation of the double bonds on the isoprenoid moiety of archaeal membranes. The structure determined in this study belongs to the p-hydroxybenzoate hydroxylase family in the glutathione reductase superfamily. GGR functions as a monomer and is divided into the FAD-binding, catalytic and C-terminal domains. The catalytic domain has a large cavity surrounded by a characteristic YxWxFPx(7-8)GxG motif and by the isoalloxazine ring of an FAD molecule. The cavity holds a lipid molecule, which is probably derived from Escherichia coli cells used for over-expression. One of the two forms of the structure clarifies the presence of an anion pocket holding a pyrophosphate molecule, which might anchor the phosphate head of the natural ligands. Mutational analysis supports the suggestion that the three aromatic residues of the YxWxFPx(7-8)GxG motif hold the ligand in the appropriate position for reduction. Cys47, which is widely conserved in GGRs, is located at the si-side of the isoalloxazine ring of FAD and is shown by mutational analysis to be involved in catalysis. The catalytic cycle, including the FAD reducing factor binding site, is proposed on the basis of the detailed analysis of the structure.

Structure and mutation analysis of archaeal geranylgeranyl reductase.,Sasaki D, Fujihashi M, Iwata Y, Murakami M, Yoshimura T, Hemmi H, Miki K J Mol Biol. 2011 Jun 17;409(4):543-57. Epub 2011 Apr 16. PMID:21515284^[4]

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

References

↑ Sato S, Murakami M, Yoshimura T, Hemmi H. Specific partial reduction of geranylgeranyl diphosphate by an enzyme from the thermoacidophilic archaeon Sulfolobus acidocaldarius yields a reactive prenyl donor, not a dead-end product. J Bacteriol. 2008 Jun;190(11):3923-9. doi: 10.1128/JB.00082-08. Epub 2008 Mar 28. PMID:18375567 doi:http://dx.doi.org/10.1128/JB.00082-08
↑ Sasaki D, Fujihashi M, Iwata Y, Murakami M, Yoshimura T, Hemmi H, Miki K. Structure and mutation analysis of archaeal geranylgeranyl reductase. J Mol Biol. 2011 Jun 17;409(4):543-57. Epub 2011 Apr 16. PMID:21515284 doi:http://dx.doi.org/10.1016/j.jmb.2011.04.002
↑ Kung Y, McAndrew RP, Xie X, Liu CC, Pereira JH, Adams PD, Keasling JD. Constructing Tailored Isoprenoid Products by Structure-Guided Modification of Geranylgeranyl Reductase. Structure. 2014 Jun 17. pii: S0969-2126(14)00148-8. doi:, 10.1016/j.str.2014.05.007. PMID:24954619 doi:http://dx.doi.org/10.1016/j.str.2014.05.007
↑ Sasaki D, Fujihashi M, Iwata Y, Murakami M, Yoshimura T, Hemmi H, Miki K. Structure and mutation analysis of archaeal geranylgeranyl reductase. J Mol Biol. 2011 Jun 17;409(4):543-57. Epub 2011 Apr 16. PMID:21515284 doi:http://dx.doi.org/10.1016/j.jmb.2011.04.002

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/3atr"

@@ Line 3: / Line 3: @@
 <StructureSection load='3atr' size='340' side='right'caption='[[3atr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3atr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33909 Atcc 33909]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ATR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ATR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3atr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ATR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ATR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3atq|3atq]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=FDA:DIHYDROFLAVINE-ADENINE+DINUCLEOTIDE'>FDA</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Saci_0986 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2285 ATCC 33909])</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=3atr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3atr OCA], [https://pdbe.org/3atr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3atr RCSB], [https://www.ebi.ac.uk/pdbsum/3atr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3atr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/GGR_SULAC GGR_SULAC] Is involved in the reduction of 2,3-digeranylgeranylglycerophospholipids (unsaturated archaeols) into 2,3-diphytanylglycerophospholipids (saturated archaeols) in the biosynthesis of archaeal membrane lipids. Catalyzes the formation of archaetidic acid (2,3-di-O-phytanyl-sn-glyceryl phosphate) from 2,3-di-O-geranylgeranylglyceryl phosphate (DGGGP) via the hydrogenation of each double bond of the isoprenoid chains. Is not active with NADPH or NADH as an electron donor; the physiological reducing agent is unknown. Is also active on the more upstream precursors of membrane lipid biosynthesis, catalyzing the complete reduction of 3-O-geranylgeranylglyceryl phosphate (GGGP) to 3-O-phytanylglyceryl phosphate, and the partial reduction of geranylgeranyl diphosphate (GGPP) to phytyl diphosphate, thus reducing three of four GGPP double bonds and preserving the allylic double bond (at position 2). This reaction product is a reactive prenyl donor, which can be used as a substrate by archaeal prenyltransferases such as GGGP synthases.<ref>PMID:18375567</ref> <ref>PMID:21515284</ref> <ref>PMID:24954619</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 33909]]
 [[Category: Large Structures]]
-[[Category: Fujihashi, M]]
+[[Category: Sulfolobus acidocaldarius]]
-[[Category: Hemmi, H]]
+[[Category: Fujihashi M]]
-[[Category: Iwata, Y]]
+[[Category: Hemmi H]]
-[[Category: Miki, K]]
+[[Category: Iwata Y]]
-[[Category: Sasaki, D]]
+[[Category: Miki K]]
-[[Category: Yoshimura, T]]
+[[Category: Sasaki D]]
-[[Category: 3-di-o-geranylgeranylglyceryl phosphate]]
+[[Category: Yoshimura T]]
-[[Category: Archaeal membrane precursor]]
-[[Category: Like 2]]
-[[Category: Oxidoreductase]]
-[[Category: Saturating double bond]]

3atr

From Proteopedia

Current revision

Geranylgeranyl Reductase (GGR) from Sulfolobus acidocaldarius co-crystallized with its ligand

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox