3e6v: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3e6v.png|left|200px]]
-<!--
+==X-ray structure of human arginase I-D183N mutant: the complex with ABH==
-The line below this paragraph, containing "STRUCTURE_3e6v", creates the "Structure Box" on the page.
+<StructureSection load='3e6v' size='340' side='right'caption='[[3e6v]], [[Resolution|resolution]] 1.72&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'>[[3e6v]] is a 2 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=3E6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E6V 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]] 1.72&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABH:2(S)-AMINO-6-BORONOHEXANOIC+ACID'>ABH</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-{{STRUCTURE_3e6v|  PDB=3e6v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e6v OCA], [https://pdbe.org/3e6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e6v RCSB], [https://www.ebi.ac.uk/pdbsum/3e6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e6v ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/ARGI1_HUMAN ARGI1_HUMAN] Defects in ARG1 are the cause of argininemia (ARGIN) [MIM:[https://omim.org/entry/207800 207800]; also known as hyperargininemia. Argininemia is a rare autosomal recessive disorder of the urea cycle. Arginine is elevated in the blood and cerebrospinal fluid, and periodic hyperammonemia occurs. Clinical manifestations include developmental delay, seizures, mental retardation, hypotonia, ataxia, progressive spastic quadriplegia.<ref>PMID:1463019</ref> <ref>PMID:7649538</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/ARGI1_HUMAN ARGI1_HUMAN]
+== 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/e6/3e6v_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=3e6v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the alpha-amino and alpha-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate alpha-carboxylate and T135, (2) a direct hydrogen bond between the substrate alpha-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate alpha-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased K(M) values but have less pronounced effects on catalytic function as reflected by minimal variations of k(cat). As with substrate K(M) values, inhibitor K(d) values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond &lt; direct hydrogen bond &lt; direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.
-===X-ray structure of human arginase I-D183N mutant: the complex with ABH===
+Probing the specificity determinants of amino acid recognition by arginase.,Shishova EY, Di Costanzo L, Emig FA, Ash DE, Christianson DW Biochemistry. 2009 Jan 13;48(1):121-31. PMID:19093830<ref>PMID:19093830</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3e6v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19093830}}, adds the Publication Abstract to the page
+*[[Arginase 3D structures|Arginase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19093830 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19093830}}
+__TOC__
+</StructureSection>
-==About this Structure==
-E6V 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=3E6V OCA].
-==Reference==
-Probing the specificity determinants of amino acid recognition by arginase., Shishova EY, Di Costanzo L, Emig FA, Ash DE, Christianson DW, Biochemistry. 2009 Jan 13;48(1):121-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19093830 19093830]
-[[Category: Arginase]]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Christianson DW]]
-[[Category: Alternative splicing]]
+[[Category: Di Costanzo L]]
-[[Category: Amino acid recognition]]
-[[Category: Amino group recognition]]
-[[Category: Arginine metabolism]]
-[[Category: Cytoplasm]]
-[[Category: Disease mutation]]
-[[Category: Hydrolase]]
-[[Category: Manganese]]
-[[Category: Metal-binding]]
-[[Category: Mutant]]
-[[Category: Phosphoprotein]]
-[[Category: Polymorphism]]
-[[Category: Urea cycle]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 11 20:12:11 2009''