1t6p

From Proteopedia

(Difference between revisions)

Revision as of 11:43, 24 December 2020

Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides

Structural highlights

1t6p is a 8 chain structure with sequence from Cbs 6016. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:	,
Related:	1t6j
Gene:	PAL (CBS 6016)
Activity:	Lyase, with EC number 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PALY_RHOTO] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The first three-dimensional structure of phenylalanine ammonia lyase (PAL) has been determined at 2.1 A resolution for PAL from Rhodosporidium toruloides. The enzyme is structurally similar to the mechanistically related histidine ammonia lyase (HAL), with PAL having an additional approximately 160 residues extending from the common fold. We propose that catalysis (including lowering the pK(a) of nonacidic C3 of l-phenylalanine for an E1cb mechanism) is potentially governed by dipole moments of seven alpha helices associated with the PAL active site (six positive poles and one negative pole). Cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, for increasing its electrophilicity. The helix dipoles appear fully compatible with a model of phenylalanine docked in the active site of PAL having the first covalent bond formed between the amino group of substrate and the methylidene group of MIO: 12 highly conserved residues (near the N termini of helices for enhancing function) are poised to serve roles in substrate recognition, MIO activation, product separation, proton donation, or polarizing electrons from the phenyl ring of substrate for activation of C3; and a highly conserved His residue (near the C terminus of the one helix that directs its negative pole toward the active site to increase the residue's basicity) is positioned to act as a general base, abstracting the pro-S hydrogen from C3 of substrate. A similar mechanism is proposed for HAL, which has a similar disposition of seven alpha helices and similar active-site residues. The helix dipoles appear incompatible with a proposed mechanism that invokes a carbocation intermediate.

Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis.,Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T Biochemistry. 2004 Sep 14;43(36):11403-16. PMID:15350127^[2]

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

References

↑ Hodgins DS. Yeast phenylalanine ammonia-lyase. Purification, properties, and the identification of catalytically essential dehydroalanine. J Biol Chem. 1971 May 10;246(9):2977-85. PMID:5102931
↑ Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T. Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry. 2004 Sep 14;43(36):11403-16. PMID:15350127 doi:http://dx.doi.org/10.1021/bi049053+

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1t6p"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==
-<StructureSection load='1t6p' size='340' side='right' caption='[[1t6p]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='1t6p' size='340' side='right'caption='[[1t6p]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1t6p]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T6P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1t6p]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T6P FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1t6j|1t6j]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t6j|1t6j]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5286 CBS 6016])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.23, 4.3.1.24 and 4.3.1.25 4.3.1.23, 4.3.1.24 and 4.3.1.25] </span></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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://pdbe.org/1t6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6p 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=1t6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6p OCA], [http://pdbe.org/1t6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t6p RCSB], [http://www.ebi.ac.uk/pdbsum/1t6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6p ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 16: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6p_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 ==See Also==
-*[[Aminomutase|Aminomutase]]
+*[[Aminomutase 3D structures|Aminomutase 3D structures]]
 == References ==
 <references/>
@@ Line 39: / Line 39: @@
 </StructureSection>
 [[Category: Cbs 6016]]
+[[Category: Large Structures]]
 [[Category: Lyase]]
 [[Category: Calabrese, J C]]

1t6p

From Proteopedia

Revision as of 11:43, 24 December 2020

Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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