5ltm: Difference between revisions

Latest revision as of 18:48, 18 October 2023

Crystal structure of phenylalanine ammonia-lyase from Anabaena variabilis (Y78F-C503S-C565S) bound to cinnamate

Structural highlights

5ltm is a 2 chain structure with sequence from Anabaena. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.413Å
Ligands:	HCI, MDO
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PAL_TRIV2 Catalyzes the non-oxidative deamination of L-phenylalanine to form trans-cinnamic acid, the first step in the phenylpropanoid pathway.^[1] ^[2]

Publication Abstract from PubMed

The suite of biological catalysts found in Nature has the potential to contribute immensely to scientific advancements, ranging from industrial biotechnology to innovations in bioenergy and medical intervention. The endeavour to obtain a catalyst of choice is, however, wrought with challenges. Herein we report the design of a structure-based annotation system for the identification of functionally similar enzymes from diverse sequence backgrounds. Focusing on an enzymatic activity with demonstrated synthetic and therapeutic relevance, five new phenylalanine ammonia lyase (PAL) enzymes were discovered and characterised with respect to their potential applications. The variation and novelty of various desirable traits seen in these previously uncharacterised enzymes demonstrates the importance of effective sequence annotation in unlocking the potential diversity that Nature provides in the search for tailored biological tools. This new method has commercial relevance as a strategy for assaying the 'evolvability' of certain enzyme features, thus streamlining and informing protein engineering efforts.

Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes.,Weise NJ, Ahmed ST, Parmeggiani F, Galman JL, Dunstan MS, Charnock SJ, Leys D, Turner NJ Sci Rep. 2017 Oct 20;7(1):13691. doi: 10.1038/s41598-017-13990-0. PMID:29057979^[3]

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

References

↑ Moffitt MC, Louie GV, Bowman ME, Pence J, Noel JP, Moore BS. Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization. Biochemistry. 2007 Jan 30;46(4):1004-12. PMID:17240984 doi:https://dx.doi.org/10.1021/bi061774g
↑ Wang L, Gamez A, Archer H, Abola EE, Sarkissian CN, Fitzpatrick P, Wendt D, Zhang Y, Vellard M, Bliesath J, Bell SM, Lemontt JF, Scriver CR, Stevens RC. Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase. J Mol Biol. 2008 Jul 18;380(4):623-35. Epub 2008 May 17. PMID:18556022 doi:https://dx.doi.org/10.1016/j.jmb.2008.05.025
↑ Weise NJ, Ahmed ST, Parmeggiani F, Galman JL, Dunstan MS, Charnock SJ, Leys D, Turner NJ. Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes. Sci Rep. 2017 Oct 20;7(1):13691. doi: 10.1038/s41598-017-13990-0. PMID:29057979 doi:https://dx.doi.org/10.1038/s41598-017-13990-0

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Moffitt MC, Louie GV, Bowman ME, Pence J, Noel JP, Moore BS. Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization. Biochemistry. 2007 Jan 30;46(4):1004-12. PMID:17240984 doi:https://dx.doi.org/10.1021/bi061774g

[2] Wang L, Gamez A, Archer H, Abola EE, Sarkissian CN, Fitzpatrick P, Wendt D, Zhang Y, Vellard M, Bliesath J, Bell SM, Lemontt JF, Scriver CR, Stevens RC. Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase. J Mol Biol. 2008 Jul 18;380(4):623-35. Epub 2008 May 17. PMID:18556022 doi:https://dx.doi.org/10.1016/j.jmb.2008.05.025

[3] Weise NJ, Ahmed ST, Parmeggiani F, Galman JL, Dunstan MS, Charnock SJ, Leys D, Turner NJ. Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes. Sci Rep. 2017 Oct 20;7(1):13691. doi: 10.1038/s41598-017-13990-0. PMID:29057979 doi:https://dx.doi.org/10.1038/s41598-017-13990-0

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='5ltm' size='340' side='right'caption='[[5ltm]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ltm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Anabaena Anabaena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LTM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LTM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ltm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anabaena Anabaena]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LTM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LTM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCI:HYDROCINNAMIC+ACID'>HCI</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]] 2.413&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HCI:HYDROCINNAMIC+ACID'>HCI</scene>, <scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene></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=5ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ltm OCA], [http://pdbe.org/5ltm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ltm RCSB], [http://www.ebi.ac.uk/pdbsum/5ltm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ltm ProSAT]</span></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=5ltm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ltm OCA], [https://pdbe.org/5ltm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ltm RCSB], [https://www.ebi.ac.uk/pdbsum/5ltm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ltm ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PAL_TRIV2 PAL_TRIV2] Catalyzes the non-oxidative deamination of L-phenylalanine to form trans-cinnamic acid, the first step in the phenylpropanoid pathway.<ref>PMID:17240984</ref> <ref>PMID:18556022</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 25: @@
 [[Category: Anabaena]]
 [[Category: Large Structures]]
-[[Category: Dunstan, M S]]
+[[Category: Dunstan MS]]
-[[Category: Leys, D]]
+[[Category: Leys D]]
-[[Category: Avpal]]
-[[Category: Cinnamate]]
-[[Category: Lyase]]
-[[Category: Phenylalanine ammonia-lyase. y78f mutant]]

5ltm: Difference between revisions

Latest revision as of 18:48, 18 October 2023

Crystal structure of phenylalanine ammonia-lyase from Anabaena variabilis (Y78F-C503S-C565S) bound to cinnamate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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