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.


3hvm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "3hvm" [edit=sysop:move=sysop])
Line 1: Line 1:
-
[[Image:3hvm.png|left|200px]]
+
==Agmatine Deiminase from Helicobacter pylori==
 +
<StructureSection load='3hvm' size='340' side='right' caption='[[3hvm]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3hvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HVM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HVM FirstGlance]. <br>
 +
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HPAG1_0045, jhp_0042 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])</td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hvm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hvm RCSB], [http://www.ebi.ac.uk/pdbsum/3hvm PDBsum]</span></td></tr>
 +
</table>
 +
== 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/hv/3hvm_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/chain_selection.php?pdb_ID=2ata ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Helicobacter pylori encodes a potential virulence factor, agmatine deiminase (HpAgD), which catalyzes the conversion of agmatine to N-carbamoyl putrescine (NCP) and ammonia - agmatine is decarboxylated arginine. Agmatine is an endogenous human cell signaling molecule that triggers the innate immune response in humans. Unlike H. pylori, humans do not encode an AgD; it is hypothesized that inhibition of this enzyme would increase the levels of agmatine, and thereby enhance the innate immune response. Taken together, these facts suggest that HpAgD is a potential drug target. Herein we describe the optimized expression, isolation, and purification of HpAgD (10-30 mg/L media). The initial kinetic characterization of this enzyme has also been performed. Additionally, the crystal structure of wild-type HpAgD has been determined at 2.1A resolution. This structure provides a molecular basis for the preferential deimination of agmatine, and identifies Asp198 as a key residue responsible for agmatine recognition, which has been confirmed experimentally. Information gathered from these studies led to the development and characterization of a novel class of haloacetamidine-based HpAgD inactivators. These compounds are the most potent AgD inhibitors ever described.
-
{{STRUCTURE_3hvm| PDB=3hvm | SCENE= }}
+
Characterization and inactivation of an agmatine deiminase from Helicobacter pylori.,Jones JE, Causey CP, Lovelace L, Knuckley B, Flick H, Lebioda L, Thompson PR Bioorg Chem. 2010 Apr;38(2):62-73. Epub 2009 Nov 29. PMID:20036411<ref>PMID:20036411</ref>
-
===Agmatine Deiminase from Helicobacter pylori===
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
{{ABSTRACT_PUBMED_20036411}}
+
== References ==
-
 
+
<references/>
-
==About this Structure==
+
__TOC__
-
[[3hvm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HVM OCA].
+
</StructureSection>
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:020036411</ref><references group="xtra"/>
+
[[Category: Helicobacter pylori]]
[[Category: Helicobacter pylori]]
-
[[Category: Jones, J.]]
+
[[Category: Jones, J]]
-
[[Category: Lebioda, L.]]
+
[[Category: Lebioda, L]]
-
[[Category: Lovelace, L.]]
+
[[Category: Lovelace, L]]
-
[[Category: Thompson, P.]]
+
[[Category: Thompson, P]]
[[Category: Agmatine deiminase]]
[[Category: Agmatine deiminase]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]

Revision as of 09:29, 8 December 2014

Agmatine Deiminase from Helicobacter pylori

3hvm, resolution 2.10Å

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/3hvm"
Personal tools