1qj5: Difference between revisions

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-[[Image:1qj5.gif|left|200px]]<br />
-<applet load="1qj5" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1qj5, resolution 1.8&Aring;" />
-'''CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE'''<br />
-==Overview==
+==Crystal structure of 7,8-diaminopelargonic acid synthase==
-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 ... [[http://ispc.weizmann.ac.il/pmbin/getpm?10452893 (full description)]]
+<StructureSection load='1qj5' size='340' side='right'caption='[[1qj5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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>
+<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>
+</table>
+== Function ==
+[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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qj/1qj5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-QJ5 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 K and PLP 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]]. Structure known Active Sites: LL1 and LL2. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QJ5 OCA]].
+*[[7%2C8-diaminopelargonic acid synthase 3D structures|7%2C8-diaminopelargonic acid synthase 3D structures]]
+== References ==
-==Reference==
+<references/>
-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]
+__TOC__
-[[Category: Adenosylmethionine--8-amino-7-oxononanoate transaminase]]
+</StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Gibson KJ]]
-[[Category: Gibson, K.J.]]
+[[Category: Kack H]]
-[[Category: Kack, H.]]
+[[Category: Lindqvist Y]]
-[[Category: Lindqvist, Y.]]
+[[Category: Sandmark J]]
-[[Category: Sandmark, J.]]
+[[Category: Schneider G]]
-[[Category: Schneider, G.]]
-[[Category: K]]
-[[Category: PLP]]
-[[Category: aminotransferase]]
-[[Category: biotin biosynthesis]]
-[[Category: pyridoxal-5'-phosphate]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 16:00:06 2007''