3vzy: Difference between revisions

Latest revision as of 12:43, 8 November 2023

Crystal structure of PcrB complexed with G1P from bacillus subtilis subap. subtilis str. 168

Structural highlights

3vzy is a 2 chain structure with sequence from Bacillus subtilis subsp. subtilis str. 168. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.63Å
Ligands:	1GP, CL, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PCRB_BACSU Prenyltransferase that catalyzes in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP). This reaction is an ether-bond-formation step in the biosynthesis of archaea-type G1P-based membrane lipids found in Bacillales. To a much lesser extent, is also able to use geranyl diphosphate (GPP; C10) and geranylgeranyl diphosphate (GGPP; C20) as the prenyl donors, but not farnesyl pyrophosphate (FPP; C15). Can not use glycerol-3-phosphate (G3P) or 3-phosphoglycerate (3PG) as an acceptor.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Well structured: As a new triose phosphate isomerase (TIM) barrel-fold prenyl transferase, PcrB catalyzes the production of heptaprenylglyceryl phosphate from heptaprenyl diphosphate and glycerol-1-phosphate. Crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus in complex with ligands were solved, and together with site-directed mutagenesis and bioinformatics analyses, clearly reveal the catalytic mechanism of the enzyme.

Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus.,Ren F, Feng X, Ko TP, Huang CH, Hu Y, Chan HC, Liu YL, Wang K, Chen CC, Pang X, He M, Li Y, Oldfield E, Guo RT Chembiochem. 2013 Jan 21;14(2):195-9. doi: 10.1002/cbic.201200748. Epub 2013 Jan , 15. PMID:23322418^[4]

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

References

↑ Guldan H, Sterner R, Babinger P. Identification and characterization of a bacterial glycerol-1-phosphate dehydrogenase: Ni(2+)-dependent AraM from Bacillus subtilis. Biochemistry. 2008 Jul 15;47(28):7376-84. Epub 2008 Jun 18. PMID:18558723 doi:10.1021/bi8005779
↑ Guldan H, Matysik FM, Bocola M, Sterner R, Babinger P. Functional assignment of an enzyme that catalyzes the synthesis of an archaea-type ether lipid in bacteria. Angew Chem Int Ed Engl. 2011 Aug 22;50(35):8188-91. doi: 10.1002/anie.201101832. , Epub 2011 Jul 14. PMID:21761520 doi:10.1002/anie.201101832
↑ Doud EH, Perlstein DL, Wolpert M, Cane DE, Walker S. Two distinct mechanisms for TIM barrel prenyltransferases in bacteria. J Am Chem Soc. 2011 Feb 9;133(5):1270-3. doi: 10.1021/ja109578b. Epub 2011 Jan 7. PMID:21214173 doi:10.1021/ja109578b
↑ Ren F, Feng X, Ko TP, Huang CH, Hu Y, Chan HC, Liu YL, Wang K, Chen CC, Pang X, He M, Li Y, Oldfield E, Guo RT. Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus. Chembiochem. 2013 Jan 21;14(2):195-9. doi: 10.1002/cbic.201200748. Epub 2013 Jan , 15. PMID:23322418 doi:10.1002/cbic.201200748

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Guldan H, Sterner R, Babinger P. Identification and characterization of a bacterial glycerol-1-phosphate dehydrogenase: Ni(2+)-dependent AraM from Bacillus subtilis. Biochemistry. 2008 Jul 15;47(28):7376-84. Epub 2008 Jun 18. PMID:18558723 doi:10.1021/bi8005779

[2] Guldan H, Matysik FM, Bocola M, Sterner R, Babinger P. Functional assignment of an enzyme that catalyzes the synthesis of an archaea-type ether lipid in bacteria. Angew Chem Int Ed Engl. 2011 Aug 22;50(35):8188-91. doi: 10.1002/anie.201101832. , Epub 2011 Jul 14. PMID:21761520 doi:10.1002/anie.201101832

[3] Doud EH, Perlstein DL, Wolpert M, Cane DE, Walker S. Two distinct mechanisms for TIM barrel prenyltransferases in bacteria. J Am Chem Soc. 2011 Feb 9;133(5):1270-3. doi: 10.1021/ja109578b. Epub 2011 Jan 7. PMID:21214173 doi:10.1021/ja109578b

[4] Ren F, Feng X, Ko TP, Huang CH, Hu Y, Chan HC, Liu YL, Wang K, Chen CC, Pang X, He M, Li Y, Oldfield E, Guo RT. Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus. Chembiochem. 2013 Jan 21;14(2):195-9. doi: 10.1002/cbic.201200748. Epub 2013 Jan , 15. PMID:23322418 doi:10.1002/cbic.201200748

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[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='3vzy' size='340' side='right'caption='[[3vzy]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vzy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VZY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vzy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VZY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1GP:SN-GLYCEROL-1-PHOSPHATE'>1GP</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]] 1.63&#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;'>[[3vzx|3vzx]], [[3vzz|3vzz]], [[3w00|3w00]], [[3w01|3w01]], [[3w02|3w02]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1GP:SN-GLYCEROL-1-PHOSPHATE'>1GP</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">pcrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=3vzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vzy OCA], [https://pdbe.org/3vzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vzy RCSB], [https://www.ebi.ac.uk/pdbsum/3vzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vzy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PCRB_BACSU PCRB_BACSU]] Prenyltransferase that catalyzes in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP). This reaction is an ether-bond-formation step in the biosynthesis of archaea-type G1P-based membrane lipids found in Bacillales. To a much lesser extent, is also able to use geranyl diphosphate (GPP; C10) and geranylgeranyl diphosphate (GGPP; C20) as the prenyl donors, but not farnesyl pyrophosphate (FPP; C15). Can not use glycerol-3-phosphate (G3P) or 3-phosphoglycerate (3PG) as an acceptor.<ref>PMID:18558723</ref> <ref>PMID:21761520</ref> <ref>PMID:21214173</ref>
+[https://www.uniprot.org/uniprot/PCRB_BACSU PCRB_BACSU] Prenyltransferase that catalyzes in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP). This reaction is an ether-bond-formation step in the biosynthesis of archaea-type G1P-based membrane lipids found in Bacillales. To a much lesser extent, is also able to use geranyl diphosphate (GPP; C10) and geranylgeranyl diphosphate (GGPP; C20) as the prenyl donors, but not farnesyl pyrophosphate (FPP; C15). Can not use glycerol-3-phosphate (G3P) or 3-phosphoglycerate (3PG) as an acceptor.<ref>PMID:18558723</ref> <ref>PMID:21761520</ref> <ref>PMID:21214173</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacsu]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
 [[Category: Large Structures]]
-[[Category: Chan, H C]]
+[[Category: Chan HC]]
-[[Category: Chen, C C]]
+[[Category: Chen CC]]
-[[Category: Feng, X]]
+[[Category: Feng X]]
-[[Category: Guo, R T]]
+[[Category: Guo RT]]
-[[Category: He, M]]
+[[Category: He M]]
-[[Category: Hu, Y]]
+[[Category: Hu Y]]
-[[Category: Huang, C H]]
+[[Category: Huang CH]]
-[[Category: Ko, T P]]
+[[Category: Ko TP]]
-[[Category: Li, Y]]
+[[Category: Li Y]]
-[[Category: Liu, Y L]]
+[[Category: Liu YL]]
-[[Category: Oldfield, E]]
+[[Category: Oldfield E]]
-[[Category: Pang, X]]
+[[Category: Pang X]]
-[[Category: Ren, F]]
+[[Category: Ren F]]
-[[Category: Wang, K]]
+[[Category: Wang K]]
-[[Category: Biosynthesis]]
-[[Category: Enzyme catalysis]]
-[[Category: Prenyltransferase]]
-[[Category: Transferase]]

3vzy: Difference between revisions

Latest revision as of 12:43, 8 November 2023

Crystal structure of PcrB complexed with G1P from bacillus subtilis subap. subtilis str. 168

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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