4hvy

From Proteopedia

(Difference between revisions)

Revision as of 08:18, 9 November 2022

A thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony Filtration

Structural highlights

4hvy is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NUD18_HUMAN Mediates the hydrolyzis of oxidized nucleoside diphosphate derivatives. Hydrolyzes 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing deoxyribo- and ribonucleoside diphosphates to the monophosphates. Hydrolyzes 8-oxo-dGDP and 8-oxo-GDP with the same efficiencies. Hydrolyzes also 8-OH-dADP and 2-OH-dADP. Exhibited no or minimal hydrolyzis activity against 8-oxo-dGTP, 8-oxo-GTP, dGTP, GTP, dGDP and GDP. Probably removes oxidized guanine nucleotides from both the DNA and RNA precursor pools.

Publication Abstract from PubMed

Protein stability is often a limiting factor in the development of commercial proteins and biopharmaceuticals, as well as for biochemical and structural studies. Unfortunately, identifying stabilizing mutations is not trivial since most are neutral or deleterious. Here we describe a high-throughput colony-based stability screen, which is a direct and biophysical read-out of intrinsic protein stability in contrast to traditional indirect activity-based methods. By combining the method with a random mutagenesis procedure, we successfully identify thermostable variants from 10 diverse and challenging proteins, including several biotechnologically important proteins such as a single-chain antibody, a commercial enzyme and an FDA-approved protein drug. We also show that thermostabilization of a protein drug using our approach translates into dramatic improvements in long-term stability. As the method is generic and activity independent, it can easily be applied to a wide range of proteins.

Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell.,Asial I, Cheng YX, Engman H, Dollhopf M, Wu B, Nordlund P, Cornvik T Nat Commun. 2013 Dec 19;4:2901. doi: 10.1038/ncomms3901. PMID:24352381^[1]

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

References

↑ Asial I, Cheng YX, Engman H, Dollhopf M, Wu B, Nordlund P, Cornvik T. Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell. Nat Commun. 2013 Dec 19;4:2901. doi: 10.1038/ncomms3901. PMID:24352381 doi:http://dx.doi.org/10.1038/ncomms3901

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/4hvy"

@@ Line 1: / Line 1: @@
 ==A thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony Filtration==
-<StructureSection load='4hvy' size='340' side='right' caption='[[4hvy]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
+<StructureSection load='4hvy' size='340' side='right'caption='[[4hvy]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4hvy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HVY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4hvy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HVY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3gg6|3gg6]]</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=4hvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hvy OCA], [https://pdbe.org/4hvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hvy RCSB], [https://www.ebi.ac.uk/pdbsum/4hvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hvy ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUDT18 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4hvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hvy OCA], [http://pdbe.org/4hvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hvy RCSB], [http://www.ebi.ac.uk/pdbsum/4hvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hvy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NUD18_HUMAN NUD18_HUMAN]] Mediates the hydrolyzis of oxidized nucleoside diphosphate derivatives. Hydrolyzes 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing deoxyribo- and ribonucleoside diphosphates to the monophosphates. Hydrolyzes 8-oxo-dGDP and 8-oxo-GDP with the same efficiencies. Hydrolyzes also 8-OH-dADP and 2-OH-dADP. Exhibited no or minimal hydrolyzis activity against 8-oxo-dGTP, 8-oxo-GTP, dGTP, GTP, dGDP and GDP. Probably removes oxidized guanine nucleotides from both the DNA and RNA precursor pools.
+[https://www.uniprot.org/uniprot/NUD18_HUMAN NUD18_HUMAN] Mediates the hydrolyzis of oxidized nucleoside diphosphate derivatives. Hydrolyzes 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing deoxyribo- and ribonucleoside diphosphates to the monophosphates. Hydrolyzes 8-oxo-dGDP and 8-oxo-GDP with the same efficiencies. Hydrolyzes also 8-OH-dADP and 2-OH-dADP. Exhibited no or minimal hydrolyzis activity against 8-oxo-dGTP, 8-oxo-GTP, dGTP, GTP, dGDP and GDP. Probably removes oxidized guanine nucleotides from both the DNA and RNA precursor pools.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Asial, I]]
+[[Category: Large Structures]]
-[[Category: Cheng, Y X]]
+[[Category: Asial I]]
-[[Category: Cornvik, T]]
+[[Category: Cheng YX]]
-[[Category: Dollhopf, M]]
+[[Category: Cornvik T]]
-[[Category: Engman, H]]
+[[Category: Dollhopf M]]
-[[Category: Nordlund, P]]
+[[Category: Engman H]]
-[[Category: Wu, B]]
+[[Category: Nordlund P]]
-[[Category: Directed evolution]]
+[[Category: Wu B]]
-[[Category: Hot colony filtration]]
-[[Category: Hot-cofi]]
-[[Category: Hydrolase]]
-[[Category: Thermostability]]

4hvy

From Proteopedia

Revision as of 08:18, 9 November 2022

A thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony Filtration

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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