3k30

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:08, 6 September 2023) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3k30.png|left|200px]]
 
-
<!--
+
==Histamine dehydrogenase from Nocardiodes simplex==
-
The line below this paragraph, containing "STRUCTURE_3k30", creates the "Structure Box" on the page.
+
<StructureSection load='3k30' size='340' side='right'caption='[[3k30]], [[Resolution|resolution]] 2.70&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'>[[3k30]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pimelobacter_simplex Pimelobacter simplex]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K30 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]] 2.7&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
-
{{STRUCTURE_3k30| PDB=3k30 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3k30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k30 OCA], [https://pdbe.org/3k30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k30 RCSB], [https://www.ebi.ac.uk/pdbsum/3k30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k30 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q6IWJ5_NOCSI Q6IWJ5_NOCSI]
 +
== 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/k3/3k30_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=3k30 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Histamine dehydrogenase (HADH) isolated from Nocardioides simplex catalyzes the oxidative deamination of histamine to imidazole acetaldehyde. HADH is highly specific for histamine, and we are interested in understanding the recognition mode of histamine in its active site. We describe the first crystal structure of a recombinant form of HADH (HADH) to 2.7-A resolution. HADH is a homodimer, where each 76-kDa subunit contains an iron-sulfur cluster ([4Fe-4S](2+)) and a 6-S-cysteinyl flavin mononucleotide (6-S-Cys-FMN) as redox cofactors. The overall structure of HADH is very similar to that of trimethylamine dehydrogenase (TMADH) from Methylotrophus methylophilus (bacterium W3A1). However, some distinct differences between the structure of HADH and TMADH have been found. Tyr(60), Trp(264), and Trp(355) provide the framework for the "aromatic bowl" that serves as a trimethylamine-binding site in TMADH is comprised of Gln(65), Trp(267), and Asp(358), respectively, in HADH. The surface Tyr(442) that is essential in transferring electrons to electron-transfer flavoprotein (ETF) in TMADH is not conserved in HADH. We use this structure to propose the binding mode for histamine in the active site of HADH through molecular modeling and to compare the interactions to those observed for other histamine-binding proteins whose structures are known.
-
===Histamine dehydrogenase from Nocardiodes simplex===
+
Crystal structure of histamine dehydrogenase from Nocardioides simplex.,Reed T, Lushington GH, Xia Y, Hirakawa H, Travis DM, Mure M, Scott EE, Limburg J J Biol Chem. 2010 Aug 13;285(33):25782-91. Epub 2010 Jun 10. PMID:20538584<ref>PMID:20538584</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20538584}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3k30" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20538584 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20538584}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
3K30 is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Pimelobacter_simplex Pimelobacter simplex]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K30 OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:20538584</ref><references group="xtra"/>
+
[[Category: Pimelobacter simplex]]
[[Category: Pimelobacter simplex]]
-
[[Category: Limburg, J.]]
+
[[Category: Limburg J]]
-
[[Category: Reed, T M.]]
+
[[Category: Reed TM]]
-
[[Category: Scott, E E.]]
+
[[Category: Scott EE]]
-
[[Category: 6-s-cysteinyl-fmn]]
+
-
[[Category: Adp binding site]]
+
-
[[Category: Oxidoreductase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 1 09:16:56 2010''
+

Current revision

Histamine dehydrogenase from Nocardiodes simplex

PDB ID 3k30

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/3k30"
Personal tools