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.


1woi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:33, 13 March 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1woi.gif|left|200px]]
 
-
{{Structure
+
==Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily==
-
|PDB= 1woi |SIZE=350|CAPTION= <scene name='initialview01'>1woi</scene>, resolution 1.85&Aring;
+
<StructureSection load='1woi' size='340' side='right'caption='[[1woi]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MN:MANGANESE (II) ION'>MN</scene>
+
<table><tr><td colspan='2'>[[1woi]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WOI FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Agmatinase Agmatinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.11 3.5.3.11]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1woi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1woi OCA], [https://pdbe.org/1woi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1woi RCSB], [https://www.ebi.ac.uk/pdbsum/1woi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1woi ProSAT]</span></td></tr>
-
 
+
</table>
-
'''Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/Q9RZ04_DEIRA Q9RZ04_DEIRA]
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Agmatine is the product of arginine decarboxylation and can be hydrolyzed by agmatinase to putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. Besides being an intermediate in polyamine metabolism, recent findings indicate that agmatine may play important regulatory roles in mammals. Agmatinase is a binuclear manganese metalloenzyme and belongs to the ureohydrolase superfamily that includes arginase, formiminoglutamase, and proclavaminate amidinohydrolase. Compared with a wealth of structural information available for arginases, no three-dimensional structure of agmatinase has been reported. Agmatinase from Deinococcus radiodurans, a 304-residue protein, shows approximately 33% of sequence identity to human mitochondrial agmatinase. Here we report the crystal structure of D. radiodurans agmatinase in Mn(2+)-free, Mn(2+)-bound, and Mn(2+)-inhibitor-bound forms, representing the first structure of agmatinase. It reveals the conservation as well as variation in folding, oligomerization, and the active site of the ureohydrolase superfamily. D. radiodurans agmatinase exists as a compact homohexamer of 32 symmetry. Its binuclear manganese cluster is highly similar but not identical to the clusters of arginase and proclavaminate amidinohydrolase. The structure of the inhibited complex reveals that inhibition by 1,6-diaminohexane arises from the displacement of the metal-bridging water.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wo/1woi_consurf.spt"</scriptWhenChecked>
-
1WOI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WOI OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily., Ahn HJ, Kim KH, Lee J, Ha JY, Lee HH, Kim D, Yoon HJ, Kwon AR, Suh SW, J Biol Chem. 2004 Nov 26;279(48):50505-13. Epub 2004 Sep 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15355972 15355972]
+
</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=1woi ConSurf].
-
[[Category: Agmatinase]]
+
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Ahn, H J.]]
+
[[Category: Ahn HJ]]
-
[[Category: Ha, J Y.]]
+
[[Category: Ha J-Y]]
-
[[Category: Kim, D.]]
+
[[Category: Kim D]]
-
[[Category: Kim, K H.]]
+
[[Category: Kim KH]]
-
[[Category: Kwon, A R.]]
+
[[Category: Kwon A-R]]
-
[[Category: Lee, H H.]]
+
[[Category: Lee HH]]
-
[[Category: Lee, J.]]
+
[[Category: Lee J]]
-
[[Category: Suh, S W.]]
+
[[Category: Suh SW]]
-
[[Category: Yoon, H J.]]
+
[[Category: Yoon H-J]]
-
[[Category: MN]]
+
-
[[Category: alpha/beta fold]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:59:38 2008''
+

Current revision

Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily

PDB ID 1woi

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/1woi"
Personal tools