6i00

From Proteopedia

(Difference between revisions)

Current revision

Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.

6i00, resolution 3.40Å

Structural highlights

6i00 is a 12 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	NIT4, At5g22300, MWD9.8 (ARATH)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NRL4_ARATH] Highly specific for beta-cyano-L-alanine (Ala(CN)). Low activity with 3-phenylpropionitrile (PPN) or allylcyanide and no activity with indole-3-acetonitrile. Not associated with auxin production but may be involved in cyanide detoxification.^[1]

Publication Abstract from PubMed

Nitrilases are helical enzymes that convert nitriles to acids and/or amides. All plants have a nitrilase 4 homolog specific for ss-cyanoalanine, while in some plants neofunctionalization has produced nitrilases with altered specificity. Plant nitrilase substrate size and specificity correlate with helical twist, but molecular details of this relationship are lacking. Here we determine, to our knowledge, the first close-to-atomic resolution (3.4 A) cryo-EM structure of an active helical nitrilase, the nitrilase 4 from Arabidopsis thaliana. We apply site-saturation mutagenesis directed evolution to three residues (R95, S224, and L169) and generate a mutant with an altered helical twist that accepts substrates not catalyzed by known plant nitrilases. We reveal that a loop between alpha2 and alpha3 limits the length of the binding pocket and propose that it shifts position as a function of helical twist. These insights will allow us to start designing nitrilases for chemoenzymatic synthesis.

Cryo-EM and directed evolution reveal how Arabidopsis nitrilase specificity is influenced by its quaternary structure.,Mulelu AE, Kirykowicz AM, Woodward JD Commun Biol. 2019 Jul 17;2:260. doi: 10.1038/s42003-019-0505-4. eCollection 2019. PMID:31341959^[2]

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

References

↑ Piotrowski M, Schonfelder S, Weiler EW. The Arabidopsis thaliana isogene NIT4 and its orthologs in tobacco encode beta-cyano-L-alanine hydratase/nitrilase. J Biol Chem. 2001 Jan 26;276(4):2616-21. Epub 2000 Nov 1. PMID:11060302 doi:http://dx.doi.org/10.1074/jbc.M007890200
↑ Mulelu AE, Kirykowicz AM, Woodward JD. Cryo-EM and directed evolution reveal how Arabidopsis nitrilase specificity is influenced by its quaternary structure. Commun Biol. 2019 Jul 17;2:260. doi: 10.1038/s42003-019-0505-4. eCollection 2019. PMID:31341959 doi:http://dx.doi.org/10.1038/s42003-019-0505-4

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/6i00"

@@ Line 3: / Line 3: @@
 <SX load='6i00' size='340' side='right' viewer='molstar' caption='[[6i00]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6i00]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I00 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I00 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6i00]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I00 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6I00 FirstGlance]. <br>
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NIT4, At5g22300, MWD9.8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=6i00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i00 OCA], [http://pdbe.org/6i00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i00 RCSB], [http://www.ebi.ac.uk/pdbsum/6i00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i00 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6i00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i00 OCA], [http://pdbe.org/6i00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i00 RCSB], [http://www.ebi.ac.uk/pdbsum/6i00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i00 ProSAT]</span></td></tr>
 </table>
 == Function ==

6i00

From Proteopedia

Current revision

Cryo-EM informed directed evolution of Nitrilase 4 leads to a change in quaternary structure.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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