1iid: Difference between revisions

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Crystal Structure of Saccharomyces cerevisiae N-myristoyltransferase with Bound S-(2-oxo)pentadecylCoA and the Octapeptide GLYASKLA

OverviewOverview

MyristoylCoA:protein N-myristoyltransferase (Nmt) attaches myristate to the N-terminal Gly residue of proteins involved in a variety of signal transduction cascades, and other critical cellular functions. To gain insight about the structural basis of substrate recognition and catalysis, we determined the structures of a binary complex of Saccharomyces cerevisiae Nmt1p with myristoylCoA to 2.2 A resolution and of a ternary complex of Nmt1p with a nonhydrolyzable myristoylCoA analogue [S-(2-oxo)pentadecylCoA] and an octapeptide substrate (GLYASKLA) to 2.5 A resolution. The binary complex reveals how myristoylCoA alters the conformation of the enzyme to promote binding of both myristoylCoA and peptide and identifies the backbone amides of F170 and L171 as an oxyanion hole which polarizes the reactive thioester carbonyl. The ternary complex structure reveals details of the enzyme's peptide binding specificity and illuminates its mechanism of acyl transfer. The N-terminal Gly ammonium is positioned in close proximity to the C-terminal carboxylate of the protein, where it is poised to undergo the required deprotonation to an amine. In this conformation, the nucleophile is 6.3 A away from the thioester carbonyl. A catalytic mechanism is proposed whereby, once deprotonation is initiated, the N-terminal Gly amine can approximate the thioester carbonyl by rotating along Psi. This motion is facilitated by a H-bond network and leads to reaction between the glycine nitrogen nucleophile and the carbonyl. Loss of CoA from the tetrahedral intermediate may be facilitated by intramolecular H-bonding of the sulfur to the adenylamine of CoA. This affords a compact leaving group and lends a role for the observed bends in the CoA structure. The absolute requirement for Gly at the N-terminus of substrates is explained by the requirement for flexible rotation of its amine.

About this StructureAbout this Structure

1IID is a Single protein structure of sequence from Saccharomyces cerevisiae with and as ligands. Active as Glycylpeptide N-tetradecanoyltransferase, with EC number 2.3.1.97 Full crystallographic information is available from OCA.

ReferenceReference

Structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoylCoA and peptide provide insights about substrate recognition and catalysis., Farazi TA, Waksman G, Gordon JI, Biochemistry. 2001 May 29;40(21):6335-43. PMID:11371195

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-[[Image:1iid.gif|left|200px]]<br /><applet load="1iid" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1iid.gif|left|200px]]<br /><applet load="1iid" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1iid, resolution 2.50&Aring;" />
 '''Crystal Structure of Saccharomyces cerevisiae N-myristoyltransferase with Bound S-(2-oxo)pentadecylCoA and the Octapeptide GLYASKLA'''<br />
 ==Overview==
-MyristoylCoA:protein N-myristoyltransferase (Nmt) attaches myristate to, the N-terminal Gly residue of proteins involved in a variety of signal, transduction cascades, and other critical cellular functions. To gain, insight about the structural basis of substrate recognition and catalysis, we determined the structures of a binary complex of Saccharomyces, cerevisiae Nmt1p with myristoylCoA to 2.2 A resolution and of a ternary, complex of Nmt1p with a nonhydrolyzable myristoylCoA analogue, [S-(2-oxo)pentadecylCoA] and an octapeptide substrate (GLYASKLA) to 2.5 A, resolution. The binary complex reveals how myristoylCoA alters the, conformation of the enzyme to promote binding of both myristoylCoA and, peptide and identifies the backbone amides of F170 and L171 as an oxyanion, hole which polarizes the reactive thioester carbonyl. The ternary complex, structure reveals details of the enzyme's peptide binding specificity and, illuminates its mechanism of acyl transfer. The N-terminal Gly ammonium is, positioned in close proximity to the C-terminal carboxylate of the, protein, where it is poised to undergo the required deprotonation to an, amine. In this conformation, the nucleophile is 6.3 A away from the, thioester carbonyl. A catalytic mechanism is proposed whereby, once, deprotonation is initiated, the N-terminal Gly amine can approximate the, thioester carbonyl by rotating along Psi. This motion is facilitated by a, H-bond network and leads to reaction between the glycine nitrogen, nucleophile and the carbonyl. Loss of CoA from the tetrahedral, intermediate may be facilitated by intramolecular H-bonding of the sulfur, to the adenylamine of CoA. This affords a compact leaving group and lends, a role for the observed bends in the CoA structure. The absolute, requirement for Gly at the N-terminus of substrates is explained by the, requirement for flexible rotation of its amine.
+MyristoylCoA:protein N-myristoyltransferase (Nmt) attaches myristate to the N-terminal Gly residue of proteins involved in a variety of signal transduction cascades, and other critical cellular functions. To gain insight about the structural basis of substrate recognition and catalysis, we determined the structures of a binary complex of Saccharomyces cerevisiae Nmt1p with myristoylCoA to 2.2 A resolution and of a ternary complex of Nmt1p with a nonhydrolyzable myristoylCoA analogue [S-(2-oxo)pentadecylCoA] and an octapeptide substrate (GLYASKLA) to 2.5 A resolution. The binary complex reveals how myristoylCoA alters the conformation of the enzyme to promote binding of both myristoylCoA and peptide and identifies the backbone amides of F170 and L171 as an oxyanion hole which polarizes the reactive thioester carbonyl. The ternary complex structure reveals details of the enzyme's peptide binding specificity and illuminates its mechanism of acyl transfer. The N-terminal Gly ammonium is positioned in close proximity to the C-terminal carboxylate of the protein, where it is poised to undergo the required deprotonation to an amine. In this conformation, the nucleophile is 6.3 A away from the thioester carbonyl. A catalytic mechanism is proposed whereby, once deprotonation is initiated, the N-terminal Gly amine can approximate the thioester carbonyl by rotating along Psi. This motion is facilitated by a H-bond network and leads to reaction between the glycine nitrogen nucleophile and the carbonyl. Loss of CoA from the tetrahedral intermediate may be facilitated by intramolecular H-bonding of the sulfur to the adenylamine of CoA. This affords a compact leaving group and lends a role for the observed bends in the CoA structure. The absolute requirement for Gly at the N-terminus of substrates is explained by the requirement for flexible rotation of its amine.
 ==About this Structure==
-IID is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with NI and NHM as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glycylpeptide_N-tetradecanoyltransferase Glycylpeptide N-tetradecanoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.97 2.3.1.97] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IID OCA].
+IID is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=NI:'>NI</scene> and <scene name='pdbligand=NHM:'>NHM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glycylpeptide_N-tetradecanoyltransferase Glycylpeptide N-tetradecanoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.97 2.3.1.97] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IID OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Saccharomyces cerevisiae]]
 [[Category: Single protein]]
-[[Category: Farazi, T.A.]]
+[[Category: Farazi, T A.]]
-[[Category: Gordon, J.I.]]
+[[Category: Gordon, J I.]]
 [[Category: Waksman, G.]]
 [[Category: NHM]]
@@ Line 21: / Line 21: @@
 [[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:25:19 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:12:09 2008''