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.


2dkb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (20:38, 20 October 2021) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2dkb.png|left|200px]]
 
-
<!--
+
==DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES==
-
The line below this paragraph, containing "STRUCTURE_2dkb", creates the "Structure Box" on the page.
+
<StructureSection load='2dkb' size='340' side='right'caption='[[2dkb]], [[Resolution|resolution]] 2.10&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'>[[2dkb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_cepacia"_burkholder_1950 "pseudomonas cepacia" burkholder 1950]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKB FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-
-->
+
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) 2,2-dialkylglycine decarboxylase (pyruvate)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.64 4.1.1.64] </span></td></tr>
-
{{STRUCTURE_2dkb| PDB=2dkb | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkb OCA], [https://pdbe.org/2dkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkb RCSB], [https://www.ebi.ac.uk/pdbsum/2dkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkb ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[[https://www.uniprot.org/uniprot/DGDA_BURCE DGDA_BURCE]] The dialkylglycine decarboxylase is of interest because it normally catalyzes both decarboxylation and amino transfer. It may be more properly described as a decarboxylating aminotransferase rather than an aminotransferring decarboxylase.
 +
== 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/dk/2dkb_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=2dkb ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The structure of the bifunctional, pyridoxal phosphate-dependent enzyme dialkylglycine decarboxylase was determined to 2.1-angstrom resolution. Model building suggests that a single cleavage site catalyzes both decarboxylation and transamination by maximizing stereoelectronic advantages and providing electrostatic and general base catalysis. The enzyme contains two binding sites for alkali metal ions. One is located near the active site and accounts for the dependence of activity on potassium ions. The other is located at the carboxyl terminus of an alpha helix. These sites help show how proteins can specifically bind alkali metals and how these ions can exert functional effects.
-
===DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES===
+
Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.,Toney MD, Hohenester E, Cowan SW, Jansonius JN Science. 1993 Aug 6;261(5122):756-9. PMID:8342040<ref>PMID:8342040</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_8342040}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2dkb" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 8342040 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_8342040}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Pseudomonas cepacia burkholder 1950]]
-
2DKB is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Burkholderia_cepacia Burkholderia cepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKB OCA].
+
[[Category: Large Structures]]
-
 
+
[[Category: Hohenester, E]]
-
==Reference==
+
[[Category: Jansonius, J N]]
-
<ref group="xtra">PMID:8342040</ref><references group="xtra"/>
+
[[Category: Toney, M D]]
-
[[Category: Burkholderia cepacia]]
+
-
[[Category: Hohenester, E.]]
+
-
[[Category: Jansonius, J N.]]
+
-
[[Category: Toney, M D.]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:15:36 2009''
+

Current revision

DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES

PDB ID 2dkb

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/2dkb"
Personal tools