1dj9: Difference between revisions

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CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.

OverviewOverview

8-Amino-7-oxononanoate synthase (also known as 7-keto-8-aminopelargonate synthase, EC 2.3.1.47) is a pyridoxal 5'-phosphate-dependent enzyme which catalyzes the decarboxylative condensation of L-alanine with pimeloyl-CoA in a stereospecific manner to form 8(S)-amino-7-oxononanoate. This is the first committed step in biotin biosynthesis. The mechanism of Escherichia coli AONS has been investigated by spectroscopic, kinetic, and crystallographic techniques. The X-ray structure of the holoenzyme has been refined at a resolution of 1.7 A (R = 18.6%, R(free) = 21. 2%) and shows that the plane of the imine bond of the internal aldimine deviates from the pyridine plane. The structure of the enzyme-product external aldimine complex has been refined at a resolution of 2.0 A (R = 21.2%, R(free) = 27.8%) and shows a rotation of the pyridine ring with respect to that in the internal aldimine, together with a significant conformational change of the C-terminal domain and subtle rearrangement of the active site hydrogen bonding. The first step in the reaction, L-alanine external aldimine formation, is rapid (k(1) = 2 x 10(4) M(-)(1) s(-)(1)). Formation of an external aldimine with D-alanine, which is not a substrate, is significantly slower (k(1) = 125 M(-)(1) s(-)(1)). Binding of D-alanine to AONS is enhanced approximately 2-fold in the presence of pimeloyl-CoA. Significant substrate quinonoid formation only occurs upon addition of pimeloyl-CoA to the preformed L-alanine external aldimine complex and is preceded by a distinct lag phase ( approximately 30 ms) which suggests that binding of the pimeloyl-CoA causes a conformational transition of the enzyme external aldimine complex. This transition, which is inferred by modeling to require a rotation around the Calpha-N bond of the external aldimine complex, promotes abstraction of the Calpha proton by Lys236. These results have been combined to form a detailed mechanistic pathway for AONS catalysis which may be applied to the other members of the alpha-oxoamine synthase subfamily.

About this StructureAbout this Structure

1DJ9 is a Single protein structure of sequence from Escherichia coli with , and as ligands. Active as 8-amino-7-oxononanoate synthase, with EC number 2.3.1.47 Full crystallographic information is available from OCA.

ReferenceReference

Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies., Webster SP, Alexeev D, Campopiano DJ, Watt RM, Alexeeva M, Sawyer L, Baxter RL, Biochemistry. 2000 Jan 25;39(3):516-28. PMID:10642176

Page seeded by OCA on Thu Feb 21 12:17:17 2008

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-[[Image:1dj9.gif|left|200px]]<br /><applet load="1dj9" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1dj9.gif|left|200px]]<br /><applet load="1dj9" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1dj9, resolution 2.00&Aring;" />
 '''CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO-8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN BIOSYNTHETIC PATHWAY.'''<br />
 ==Overview==
--Amino-7-oxononanoate synthase (also known as 7-keto-8-aminopelargonate, synthase, EC 2.3.1.47) is a pyridoxal 5'-phosphate-dependent enzyme which, catalyzes the decarboxylative condensation of L-alanine with pimeloyl-CoA, in a stereospecific manner to form 8(S)-amino-7-oxononanoate. This is the, first committed step in biotin biosynthesis. The mechanism of Escherichia, coli AONS has been investigated by spectroscopic, kinetic, and, crystallographic techniques. The X-ray structure of the holoenzyme has, been refined at a resolution of 1.7 A (R = 18.6%, R(free) = 21. 2%) and, shows that the plane of the imine bond of the internal aldimine deviates, from the pyridine plane. The structure of the enzyme-product external, aldimine complex has been refined at a resolution of 2.0 A (R = 21.2%, R(free) = 27.8%) and shows a rotation of the pyridine ring with respect to, that in the internal aldimine, together with a significant conformational, change of the C-terminal domain and subtle rearrangement of the active, site hydrogen bonding. The first step in the reaction, L-alanine external, aldimine formation, is rapid (k(1) = 2 x 10(4) M(-)(1) s(-)(1)). Formation, of an external aldimine with D-alanine, which is not a substrate, is, significantly slower (k(1) = 125 M(-)(1) s(-)(1)). Binding of D-alanine to, AONS is enhanced approximately 2-fold in the presence of pimeloyl-CoA., Significant substrate quinonoid formation only occurs upon addition of, pimeloyl-CoA to the preformed L-alanine external aldimine complex and is, preceded by a distinct lag phase ( approximately 30 ms) which suggests, that binding of the pimeloyl-CoA causes a conformational transition of the, enzyme external aldimine complex. This transition, which is inferred by, modeling to require a rotation around the Calpha-N bond of the external, aldimine complex, promotes abstraction of the Calpha proton by Lys236., These results have been combined to form a detailed mechanistic pathway, for AONS catalysis which may be applied to the other members of the, alpha-oxoamine synthase subfamily.
+-Amino-7-oxononanoate synthase (also known as 7-keto-8-aminopelargonate synthase, EC 2.3.1.47) is a pyridoxal 5'-phosphate-dependent enzyme which catalyzes the decarboxylative condensation of L-alanine with pimeloyl-CoA in a stereospecific manner to form 8(S)-amino-7-oxononanoate. This is the first committed step in biotin biosynthesis. The mechanism of Escherichia coli AONS has been investigated by spectroscopic, kinetic, and crystallographic techniques. The X-ray structure of the holoenzyme has been refined at a resolution of 1.7 A (R = 18.6%, R(free) = 21. 2%) and shows that the plane of the imine bond of the internal aldimine deviates from the pyridine plane. The structure of the enzyme-product external aldimine complex has been refined at a resolution of 2.0 A (R = 21.2%, R(free) = 27.8%) and shows a rotation of the pyridine ring with respect to that in the internal aldimine, together with a significant conformational change of the C-terminal domain and subtle rearrangement of the active site hydrogen bonding. The first step in the reaction, L-alanine external aldimine formation, is rapid (k(1) = 2 x 10(4) M(-)(1) s(-)(1)). Formation of an external aldimine with D-alanine, which is not a substrate, is significantly slower (k(1) = 125 M(-)(1) s(-)(1)). Binding of D-alanine to AONS is enhanced approximately 2-fold in the presence of pimeloyl-CoA. Significant substrate quinonoid formation only occurs upon addition of pimeloyl-CoA to the preformed L-alanine external aldimine complex and is preceded by a distinct lag phase ( approximately 30 ms) which suggests that binding of the pimeloyl-CoA causes a conformational transition of the enzyme external aldimine complex. This transition, which is inferred by modeling to require a rotation around the Calpha-N bond of the external aldimine complex, promotes abstraction of the Calpha proton by Lys236. These results have been combined to form a detailed mechanistic pathway for AONS catalysis which may be applied to the other members of the alpha-oxoamine synthase subfamily.
 ==About this Structure==
-DJ9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with SO4, MG and KAM as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/8-amino-7-oxononanoate_synthase 8-amino-7-oxononanoate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.47 2.3.1.47] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DJ9 OCA].
+DJ9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=KAM:'>KAM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/8-amino-7-oxononanoate_synthase 8-amino-7-oxononanoate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.47 2.3.1.47] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJ9 OCA].
 ==Reference==
@@ Line 16: / Line 16: @@
 [[Category: Alexeev, D.]]
 [[Category: Alexeeva, M.]]
-[[Category: Baxter, R.L.]]
+[[Category: Baxter, R L.]]
-[[Category: Campopiano, D.J.]]
+[[Category: Campopiano, D J.]]
 [[Category: Sawyer, L.]]
-[[Category: Watt, R.M.]]
+[[Category: Watt, R M.]]
-[[Category: Webster, S.P.]]
+[[Category: Webster, S P.]]
 [[Category: KAM]]
 [[Category: MG]]
 [[Category: SO4]]
-[[Category: 8-amino-7-oxononanoate synthase]]
 [[Category: biotin]]
 [[Category: pyridoxal-5'-phosphate]]
 [[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:19:33 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:17:17 2008''