1t6p: Difference between revisions

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Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides

OverviewOverview

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.

About this StructureAbout this Structure

1T6P is a Single protein structure of sequence from Rhodosporidium toruloides. Active as Phenylalanine ammonia-lyase, with EC number 4.3.1.5 Full crystallographic information is available from OCA.

ReferenceReference

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

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-[[Image:1t6p.gif|left|200px]]<br /><applet load="1t6p" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1t6p, resolution 2.70&Aring;" />
 '''Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-T6P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Active as [http://en.wikipedia.org/wiki/Phenylalanine_ammonia-lyase Phenylalanine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.5 4.3.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1T6P OCA].
+T6P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Active as [http://en.wikipedia.org/wiki/Phenylalanine_ammonia-lyase Phenylalanine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.5 4.3.1.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6P OCA].
 ==Reference==
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 [[Category: Rhodosporidium toruloides]]
 [[Category: Single protein]]
-[[Category: Calabrese, J.C.]]
+[[Category: Calabrese, J C.]]
-[[Category: Jordan, D.B.]]
+[[Category: Jordan, D B.]]
 [[Category: triple helix coiled coil; mio; cinnamate]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:01:43 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:10:30 2008''