This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4gsa

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:48, 3 April 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:4gsa.jpg|left|200px]]<br /><applet load="4gsa" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="4gsa, resolution 2.50&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE==
-
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.
+
<StructureSection load='4gsa' size='340' side='right'caption='[[4gsa]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[4gsa]] 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=4GSA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GSA 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]] 2.5&#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></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=4gsa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gsa OCA], [https://pdbe.org/4gsa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gsa RCSB], [https://www.ebi.ac.uk/pdbsum/4gsa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gsa 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/4gsa_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=4gsa ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
4GSA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.] with <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glutamate-1-semialdehyde_2,1-aminomutase Glutamate-1-semialdehyde 2,1-aminomutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.3.8 5.4.3.8] Known structural/functional Sites: <scene name='pdbsite=COA:Reduced+Schiff+Base+Linkage+To+LYS+273+In+Chain+A'>COA</scene> and <scene name='pdbsite=COB:Reduced+Schiff+Base+Linkage+To+LYS+273+In+Chain+B'>COB</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GSA OCA].
+
*[[Aminomutase 3D structures|Aminomutase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9144156 9144156]
+
[[Category: Large Structures]]
-
[[Category: Glutamate-1-semialdehyde 2,1-aminomutase]]
+
[[Category: Synechococcus sp]]
-
[[Category: Single protein]]
+
[[Category: Hennig M]]
-
[[Category: Synechococcus sp.]]
+
[[Category: Jansonius JN]]
-
[[Category: Hennig, M.]]
+
-
[[Category: Jansonius, J N.]]
+
-
[[Category: PLP]]
+
-
[[Category: asymmetric dimer]]
+
-
[[Category: chlorophyll biosynthesis]]
+
-
[[Category: pyridoxal-5'-phosphate]]
+
-
[[Category: pyridoxamine-5'-phosphate]]
+
-
[[Category: reduced form]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:13:26 2008''
+

Current revision

CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE

PDB ID 4gsa

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4gsa"
Personal tools