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1qj5

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[[Image:1qj5.jpg|left|200px]]<br /><applet load="1qj5" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1qj5, resolution 1.8&Aring;" />
 
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'''CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE'''<br />
 
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==Overview==
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==Crystal structure of 7,8-diaminopelargonic acid synthase==
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The three-dimensional structure of diaminopelargonic acid synthase, a, vitamin B6-dependent enzyme in the pathway of the biosynthesis of biotin, has been determined to 1.8 A resolution by X-ray crystallography. The, structure was solved by multi-wavelength anomalous diffraction techniques, using a crystal derivatized with mercury ions. The protein model has been, refined to a crystallographic R -value of 17.5% (R -free 22.6%). Each, enzyme subunit consists of two domains, a large domain (residues 50-329), containing a seven-stranded predominantly parallel beta-sheet, surrounded, by alpha-helices, and a small domain comprising residues 1-49 and 330-429., Two subunits, related by a non-crystallographic dyad in the crystals, form, the homodimeric molecule, which contains two equal active sites., Pyridoxal-5'-phosphate is bound in a cleft formed by both domains of one, subunit and the large domain of the second subunit. The cofactor is, anchored to the enzyme by a covalent linkage to the side-chain of the, invariant residue Lys274. The phosphate group interacts with main-chain, nitrogen atoms and the side-chain of Ser113, located at the N terminus of, an alpha-helix. The pyridine nitrogen forms a hydrogen bond to the, side-chain of the invariant residue Asp245. Electron density corresponding, to a metal ion, most likely Na(+), was found in a tight turn at the, surface of the enzyme. Structure analysis reveals that diaminopelargonic, acid synthase belongs to the family of vitamin B6-dependent, aminotransferases with the same fold as originally observed in aspartate, aminotransferase. A multiple structure alignment of enzymes in this family, indicated that they form at least six different subclasses. Striking, differences in the fold of the N-terminal part of the polypeptide chain, are one of the hallmarks of these subclasses. Diaminopelargonic acid, synthase is a member of the aminotransferase subclass III. From the, structure of the non-productive complex of the holoenzyme with the, substrate 7-keto-8-aminopelargonic acid the location of the active site, and residues involved in substrate binding have been identified.
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<StructureSection load='1qj5' size='340' side='right'caption='[[1qj5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1qj5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QJ5 FirstGlance]. <br>
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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]] 1.8&#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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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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=1qj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qj5 OCA], [https://pdbe.org/1qj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qj5 RCSB], [https://www.ebi.ac.uk/pdbsum/1qj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qj5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BIOA_ECOLI BIOA_ECOLI] Catalyzes the transfer of the alpha-amino group from S-adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form 7,8-diaminopelargonic acid (DAPA). It is the only animotransferase known to utilize SAM as an amino donor.<ref>PMID:1092681</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/qj/1qj5_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=1qj5 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1QJ5 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=K:'>K</scene> and <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Adenosylmethionine--8-amino-7-oxononanoate_transaminase Adenosylmethionine--8-amino-7-oxononanoate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.62 2.6.1.62] Known structural/functional Sites: <scene name='pdbsite=LL1:Pyridoxal-5'-Phosphate+Binding+Site'>LL1</scene> and <scene name='pdbsite=LL2:Pyridoxal-5'-Phosphate+Binding+Site'>LL2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QJ5 OCA].
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*[[7%2C8-diaminopelargonic acid synthase 3D structures|7%2C8-diaminopelargonic acid synthase 3D structures]]
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== References ==
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==Reference==
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<references/>
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Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes., Kack H, Sandmark J, Gibson K, Schneider G, Lindqvist Y, J Mol Biol. 1999 Aug 27;291(4):857-76. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10452893 10452893]
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__TOC__
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[[Category: Adenosylmethionine--8-amino-7-oxononanoate transaminase]]
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</StructureSection>
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[[Category: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Gibson KJ]]
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[[Category: Gibson, K.J.]]
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[[Category: Kack H]]
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[[Category: Kack, H.]]
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[[Category: Lindqvist Y]]
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[[Category: Lindqvist, Y.]]
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[[Category: Sandmark J]]
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[[Category: Sandmark, J.]]
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[[Category: Schneider G]]
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[[Category: Schneider, G.]]
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[[Category: K]]
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[[Category: PLP]]
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[[Category: aminotransferase]]
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[[Category: biotin biosynthesis]]
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[[Category: pyridoxal-5'-phosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:00:24 2008''
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Current revision

Crystal structure of 7,8-diaminopelargonic acid synthase

PDB ID 1qj5

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