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5tkr

From Proteopedia

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Crystal structure of a Lipomyces starkeyi levoglucosan kinase G359R mutant

Structural highlights

5tkr is a 1 chain structure with sequence from Lipomyces starkeyi. 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

LGK_LIPST Levoglucosan kinase that catalyzes the transfer of a phosphate group from ATP to levoglucosan (1,6-anhydro-beta-D-glucopyranose, LG) to yield glucose 6-phosphate in the presence of magnesium ion and ATP (Ref.1, PubMed:21719279, PubMed:26354439). In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O-6 atom (Ref.1, PubMed:21719279, PubMed:26354439).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Proteins are marginally stable, and an understanding of the sequence determinants for improved protein solubility is highly desired. For enzymes, it is well known that many mutations that increase protein solubility decrease catalytic activity. These competing effects frustrate efforts to design and engineer stable, active enzymes without laborious high-throughput activity screens. To address the trade-off between enzyme solubility and activity, we performed deep mutational scanning using two different screens/selections that purport to gauge protein solubility for two full-length enzymes. We assayed a TEM-1 beta-lactamase variant and levoglucosan kinase (LGK) using yeast surface display (YSD) screening and a twin-arginine translocation pathway selection. We then compared these scans with published experimental fitness landscapes. Results from the YSD screen could explain 37% of the variance in the fitness landscapes for one enzyme. Five percent to 10% of all single missense mutations improve solubility, matching theoretical predictions of global protein stability. For a given solubility-enhancing mutation, the probability that it would retain wild-type fitness was correlated with evolutionary conservation and distance to active site, and anticorrelated with contact number. Hybrid classification models were developed that could predict solubility-enhancing mutations that maintain wild-type fitness with an accuracy of 90%. The downside of using such classification models is the removal of rare mutations that improve both fitness and solubility. To reveal the biophysical basis of enhanced protein solubility and function, we determined the crystallographic structure of one such LGK mutant. Beyond fundamental insights into trade-offs between stability and activity, these results have potential biotechnological applications.

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning.,Klesmith JR, Bacik JP, Wrenbeck EE, Michalczyk R, Whitehead TA Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2265-2270. doi:, 10.1073/pnas.1614437114. Epub 2017 Feb 14. PMID:28196882^[4]

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

References

↑ Layton DS, Ajjarapu A, Choi DW, Jarboe LR. Engineering ethanologenic Escherichia coli for levoglucosan utilization. Bioresour Technol. 2011 Sep;102(17):8318-22. PMID:21719279 doi:10.1016/j.biortech.2011.06.011
↑ Bacik JP, Klesmith JR, Whitehead TA, Jarboe LR, Unkefer CJ, Mark BL, Michalczyk R. Producing glucose-6-phosphate from cellulosic biomass: structural insights into levoglucosan bioconversion. J Biol Chem. 2015 Sep 9. pii: jbc.M115.674614. PMID:26354439 doi:http://dx.doi.org/10.1074/jbc.M115.674614
↑ Layton DS, Ajjarapu A, Choi DW, Jarboe LR. Engineering ethanologenic Escherichia coli for levoglucosan utilization. Bioresour Technol. 2011 Sep;102(17):8318-22. PMID:21719279 doi:10.1016/j.biortech.2011.06.011
↑ Klesmith JR, Bacik JP, Wrenbeck EE, Michalczyk R, Whitehead TA. Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning. Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):2265-2270. doi:, 10.1073/pnas.1614437114. Epub 2017 Feb 14. PMID:28196882 doi:http://dx.doi.org/10.1073/pnas.1614437114

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/5tkr"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a Lipomyces starkeyi levoglucosan kinase G359R mutant==
-<StructureSection load='5tkr' size='340' side='right' caption='[[5tkr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='5tkr' size='340' side='right'caption='[[5tkr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5tkr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_1807 Cbs 1807]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TKR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TKR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5tkr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lipomyces_starkeyi Lipomyces starkeyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TKR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.8&#8491;</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=5tkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tkr OCA], [http://pdbe.org/5tkr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tkr RCSB], [http://www.ebi.ac.uk/pdbsum/5tkr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tkr ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5tkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tkr OCA], [https://pdbe.org/5tkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tkr RCSB], [https://www.ebi.ac.uk/pdbsum/5tkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tkr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LGK_LIPST LGK_LIPST] Levoglucosan kinase that catalyzes the transfer of a phosphate group from ATP to levoglucosan (1,6-anhydro-beta-D-glucopyranose, LG) to yield glucose 6-phosphate in the presence of magnesium ion and ATP (Ref.1, PubMed:21719279, PubMed:26354439). In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O-6 atom (Ref.1, PubMed:21719279, PubMed:26354439).<ref>PMID:21719279</ref> <ref>PMID:26354439</ref> <ref>PMID:21719279</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Cbs 1807]]
+[[Category: Large Structures]]
-[[Category: Bacik, J P]]
+[[Category: Lipomyces starkeyi]]
-[[Category: Klesmith, J R]]
+[[Category: Bacik JP]]
-[[Category: Michalczyk, R]]
+[[Category: Klesmith JR]]
-[[Category: Whitehead, T A]]
+[[Category: Michalczyk R]]
-[[Category: Atp-binding]]
+[[Category: Whitehead TA]]
-[[Category: Carbohydrate metabolism]]
-[[Category: Levoglucosan]]
-[[Category: Mutant]]
-[[Category: Sugar kinase]]
-[[Category: Transferase]]

5tkr

From Proteopedia

Current revision

Crystal structure of a Lipomyces starkeyi levoglucosan kinase G359R mutant

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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