1dj9: Difference between revisions
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|PDB= 1dj9 |SIZE=350|CAPTION= <scene name='initialview01'>1dj9</scene>, resolution 2.00Å | |PDB= 1dj9 |SIZE=350|CAPTION= <scene name='initialview01'>1dj9</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=KAM:N-[7-KETO-8-AMINOPELARGONIC+ACID]-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>KAM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1bs0|1BS0]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dj9 OCA], [http://www.ebi.ac.uk/pdbsum/1dj9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dj9 RCSB]</span> | |||
}} | }} | ||
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[[Category: Watt, R M.]] | [[Category: Watt, R M.]] | ||
[[Category: Webster, S P.]] | [[Category: Webster, S P.]] | ||
[[Category: biotin]] | [[Category: biotin]] | ||
[[Category: pyridoxal-5'-phosphate]] | [[Category: pyridoxal-5'-phosphate]] | ||
[[Category: transferase]] | [[Category: transferase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:42:34 2008'' | ||
Revision as of 19:42, 30 March 2008
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| , resolution 2.00Å | |||||||
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| Ligands: | , , | ||||||
| Activity: | 8-amino-7-oxononanoate synthase, with EC number 2.3.1.47 | ||||||
| Related: | 1BS0
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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. 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
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