1jdx: Difference between revisions

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-[[Image:1jdx.jpg|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH L-NORVALINE==
-The line below this paragraph, containing "STRUCTURE_1jdx", creates the "Structure Box" on the page.
+<StructureSection load='1jdx' size='340' side='right'caption='[[1jdx]], [[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'>[[1jdx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JDX 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=NVA:NORVALINE'>NVA</scene></td></tr>
-{{STRUCTURE_1jdx|  PDB=1jdx  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jdx OCA], [https://pdbe.org/1jdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jdx RCSB], [https://www.ebi.ac.uk/pdbsum/1jdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jdx ProSAT]</span></td></tr>
+</table>
-'''CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH L-NORVALINE'''
+== Disease ==
+[https://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN] Defects in GATM are the cause of arginine:glycine amidinotransferase deficiency (AGAT deficiency) [MIM:[https://omim.org/entry/612718 612718]. AGAT deficiency is an autosomal recessive disorder characterized by developmental delay/regression, mental retardation, severe disturbance of expressive and cognitive speech, and severe depletion of creatine/phosphocreatine in the brain.
+== Function ==
-==Overview==
+[https://www.uniprot.org/uniprot/GATM_HUMAN GATM_HUMAN] Catalyzes the biosynthesis of guanidinoacetate, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues. May play a role in embryonic and central nervous system development. May be involved in the response to heart failure by elevating local creatine synthesis.<ref>PMID:16820567</ref> <ref>PMID:16125225</ref> <ref>PMID:16614068</ref>
-Human L-arginine:glycine amidinotransferase (AT) shows large structural changes of the 300-flap and of helix H9 upon binding of L-arginine and L-ornithine, described as a closed and an open conformation (Humm, A., Fritsche, E., Steinbacher, S., and Huber, R. (1997) EMBO J. 16, 3373-3385). To elucidate the structural basis of these induced-fit movements, the x-ray structures of AT in complex with the amidino acceptor glycine and its analogs gamma-aminobutyric acid and delta-aminovaleric acid, as well as in complex with the amidino donor analogs L-alanine, L-alpha-aminobutyric acid, and L-norvaline, have been solved at 2.6-, 2.5-, 2.37-, 2.3-, 2.5-, and 2.4-A resolutions, respectively. The latter three compounds were found to stabilize the open conformer. The glycine analogs bind in a distinct manner and do not induce the transition to the open state. The complex with glycine revealed a third binding mode, reflecting the rather broad substrate specificity of AT. These findings identified a role for the alpha-amino group of the ligand in stabilizing the open conformer. The kinetic, structural, and thermodynamic properties of the mutants ATDeltaM302 and ATDelta11 (lacks 11 residues of H9) confirmed the key role of Asn300 and suggest that in mammalian amidinotransferases, the role of helix H9 is in accelerating amidino transfer by an induced-fit mechanism. Helix H9 does not add to the stability of the protein.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
-==About this Structure==
+Check<jmol>
-JDX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JDX OCA].
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/1jdx_consurf.spt"</scriptWhenChecked>
-==Reference==
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study., Fritsche E, Humm A, Huber R, J Biol Chem. 1999 Jan 29;274(5):3026-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9915841 9915841]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: Glycine amidinotransferase]]
+  </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=1jdx ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Fritsche, E.]]
+[[Category: Fritsche E]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Humm, A.]]
+[[Category: Humm A]]
-[[Category: Catalytic triad]]
-[[Category: Creatine biosynthesis]]
-[[Category: Fivefold pseudosymmetry]]
-[[Category: Novel fold]]
-[[Category: Reaction mechanism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 21:06:21 2008''