1dj9

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(New page: 200px<br /><applet load="1dj9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dj9, resolution 2.00&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1dj9.gif|left|200px]]<br /><applet load="1dj9" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dj9, resolution 2.00&Aring;" />
 
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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.'''<br />
 
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==Overview==
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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.==
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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.
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<StructureSection load='1dj9' size='340' side='right'caption='[[1dj9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1dj9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJ9 FirstGlance]. <br>
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1DJ9 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].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dj9 OCA], [https://pdbe.org/1dj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dj9 RCSB], [https://www.ebi.ac.uk/pdbsum/1dj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dj9 ProSAT]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10642176 10642176]
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</table>
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[[Category: 8-amino-7-oxononanoate synthase]]
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== Function ==
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[https://www.uniprot.org/uniprot/BIOF_ECOLI BIOF_ECOLI] Catalyzes the decarboxylative condensation of pimeloyl-[acyl-carrier protein] and L-alanine to produce 8-amino-7-oxononanoate (AON), [acyl-carrier protein], and carbon dioxide. Can also use pimeloyl-CoA instead of pimeloyl-ACP as substrate, but it is believed that pimeloyl-ACP rather than pimeloyl-CoA is the physiological substrate of BioF.<ref>PMID:20693992</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dj/1dj9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dj9 ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Alexeev, D.]]
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[[Category: Alexeev D]]
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[[Category: Alexeeva, M.]]
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[[Category: Alexeeva M]]
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[[Category: Baxter, R.L.]]
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[[Category: Baxter RL]]
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[[Category: Campopiano, D.J.]]
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[[Category: Campopiano DJ]]
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[[Category: Sawyer, L.]]
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[[Category: Sawyer L]]
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[[Category: Watt, R.M.]]
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[[Category: Watt RM]]
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[[Category: Webster, S.P.]]
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[[Category: Webster SP]]
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[[Category: KAM]]
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[[Category: MG]]
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[[Category: SO4]]
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[[Category: 8-amino-7-oxononanoate synthase]]
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[[Category: biotin]]
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[[Category: pyridoxal-5'-phosphate]]
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[[Category: transferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:19:33 2007''
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Current revision

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.

PDB ID 1dj9

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