2gsa: Difference between revisions

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-{{Seed}}
-[[Image:2gsa.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM)==
-The line below this paragraph, containing "STRUCTURE_2gsa", creates the "Structure Box" on the page.
+<StructureSection load='2gsa' size='340' side='right'caption='[[2gsa]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2gsa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GSA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GSA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>
-{{STRUCTURE_2gsa|  PDB=2gsa  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gsa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gsa OCA], [https://pdbe.org/2gsa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gsa RCSB], [https://www.ebi.ac.uk/pdbsum/2gsa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gsa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GSA_SYNP6 GSA_SYNP6]
+== 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/gs/2gsa_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=2gsa ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of glutamate-1-semialdehyde aminomutase (EC 5.4.3.8), an alpha2-dimeric enzyme from Synechococcus, has been determined by x-ray crystallography using heavy atom derivative phasing. The structure, refined at 2.4-A resolution to an R-factor of 18.7% and good stereochemistry, explains many of the enzyme's unusual specificity and functional properties. The overall fold is that of aspartate aminotransferase and related B6 enzymes, but it also has specific features. The structure of the complex with gabaculine, a substrate analogue, shows unexpectedly that the substrate binding site involves residues from the N-terminal domain of the molecule, notably Arg-32. Glu-406 is suitably positioned to repel alpha-carboxylic acids, thereby suggesting a basis for the enzyme's reaction specificity. The subunits show asymmetry in cofactor binding and in the mobilities of the residues 153-181. In the unliganded enzyme, one subunit has the cofactor bound as an aldimine of pyridoxal phosphate with Lys-273 and, in this subunit, residues 153-181 are disordered. In the other subunit in which the cofactor is not covalently bound, residues 153-181 are well defined. Consistent with the crystallographically demonstrated asymmetry, a form of the enzyme in which both subunits have pyridoxal phosphate bound to Lys-273 through a Schiff base showed biphasic reduction by borohydride in solution. Analysis of absorption spectra during reduction provided evidence of communication between the subunits. The crystal structure of the reduced form of the enzyme shows that, despite identical cofactor binding in each monomer, the structural asymmetry at residues 153-181 remains.
-===CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM)===
+Crystal structure of glutamate-1-semialdehyde aminomutase: an alpha2-dimeric vitamin B6-dependent enzyme with asymmetry in structure and active site reactivity.,Hennig M, Grimm B, Contestabile R, John RA, Jansonius JN Proc Natl Acad Sci U S A. 1997 May 13;94(10):4866-71. PMID:9144156<ref>PMID:9144156</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2gsa" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9144156}}, adds the Publication Abstract to the page
+*[[Aminomutase 3D structures|Aminomutase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9144156 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9144156}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-GSA is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GSA OCA].
+[[Category: Synechococcus sp]]
+[[Category: Hennig M]]
-==Reference==
+[[Category: Jansonius JN]]
-<ref group="xtra">PMID:9144156</ref><references group="xtra"/>
-[[Category: Glutamate-1-semialdehyde 2,1-aminomutase]]
-[[Category: Synechococcus sp.]]
-[[Category: Hennig, M.]]
-[[Category: Jansonius, J N.]]
-[[Category: Asymmetric dimer]]
-[[Category: Chlorophyll biosynthesis]]
-[[Category: Pyridoxal-5'-phosphate]]
-[[Category: Pyridoxamine-5'-phosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:59:44 2009''