1p8q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:40, 16 August 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1p8q.gif|left|200px]]<br /><applet load="1p8q" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1p8q, resolution 2.95&Aring;" />
 
-
'''Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Cluster of Arginase I.'''<br />
 
-
==Overview==
+
==Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Cluster of Arginase I.==
 +
<StructureSection load='1p8q' size='340' side='right'caption='[[1p8q]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1p8q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P8Q 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]] 2.95&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1p8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p8q OCA], [https://pdbe.org/1p8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p8q RCSB], [https://www.ebi.ac.uk/pdbsum/1p8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p8q ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/ARGI1_RAT ARGI1_RAT]
 +
== 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/p8/1p8q_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=1p8q ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
Arginase is a binuclear manganese metalloenzyme that hydrolyzes l-arginine to form l-ornithine and urea. The three-dimensional structures of D128E, D128N, D232A, D232C, D234E, H101N, and H101E arginases I have been determined by X-ray crystallographic methods to elucidate the roles of the first-shell metal ligands in the stability and catalytic activity of the enzyme. This work represents the first structure-based dissection of the binuclear manganese cluster using site-directed mutagenesis and X-ray crystallography. Substitution of the metal ligands compromises the catalytic activity of the enzyme, either by the loss or disruption of the metal cluster or the nucleophilic metal-bridging hydroxide ion. However, the substitution of the metal ligands or the reduction of Mn(2+)(A) or Mn(2+)(B) occupancy does not compromise enzyme-substrate affinity as reflected by K(M), which remains relatively invariant across this series of arginase variants. This implicates a nonmetal binding site for substrate l-arginine in the precatalytic Michaelis complex, as proposed based on analysis of the native enzyme structure (Kanyo, Z. F., Scolnick, L. R., Ash, D. E., and Christianson, D. W. (1996) Nature 383, 554-557).
Arginase is a binuclear manganese metalloenzyme that hydrolyzes l-arginine to form l-ornithine and urea. The three-dimensional structures of D128E, D128N, D232A, D232C, D234E, H101N, and H101E arginases I have been determined by X-ray crystallographic methods to elucidate the roles of the first-shell metal ligands in the stability and catalytic activity of the enzyme. This work represents the first structure-based dissection of the binuclear manganese cluster using site-directed mutagenesis and X-ray crystallography. Substitution of the metal ligands compromises the catalytic activity of the enzyme, either by the loss or disruption of the metal cluster or the nucleophilic metal-bridging hydroxide ion. However, the substitution of the metal ligands or the reduction of Mn(2+)(A) or Mn(2+)(B) occupancy does not compromise enzyme-substrate affinity as reflected by K(M), which remains relatively invariant across this series of arginase variants. This implicates a nonmetal binding site for substrate l-arginine in the precatalytic Michaelis complex, as proposed based on analysis of the native enzyme structure (Kanyo, Z. F., Scolnick, L. R., Ash, D. E., and Christianson, D. W. (1996) Nature 383, 554-557).
-
==About this Structure==
+
Structural and functional importance of first-shell metal ligands in the binuclear manganese cluster of arginase I.,Cama E, Emig FA, Ash DE, Christianson DW Biochemistry. 2003 Jul 1;42(25):7748-58. PMID:12820884<ref>PMID:12820884</ref>
-
1P8Q is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=MN:'>MN</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Arginase Arginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.1 3.5.3.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P8Q OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structural and functional importance of first-shell metal ligands in the binuclear manganese cluster of arginase I., Cama E, Emig FA, Ash DE, Christianson DW, Biochemistry. 2003 Jul 1;42(25):7748-58. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12820884 12820884]
+
</div>
-
[[Category: Arginase]]
+
<div class="pdbe-citations 1p8q" style="background-color:#fffaf0;"></div>
-
[[Category: Rattus norvegicus]]
+
-
[[Category: Single protein]]
+
-
[[Category: Ash, D E.]]
+
-
[[Category: Cama, E.]]
+
-
[[Category: Christianson, D W.]]
+
-
[[Category: Emig, F A.]]
+
-
[[Category: GOL]]
+
-
[[Category: MN]]
+
-
[[Category: arginine metabolism]]
+
-
[[Category: binuclear manganese cluster]]
+
-
[[Category: hydrolase]]
+
-
[[Category: urea cycle]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:26:23 2008''
+
==See Also==
 +
*[[Arginase 3D structures|Arginase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Rattus norvegicus]]
 +
[[Category: Ash DE]]
 +
[[Category: Cama E]]
 +
[[Category: Christianson DW]]
 +
[[Category: Emig FA]]

Current revision

Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Cluster of Arginase I.

PDB ID 1p8q

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools