2e1y

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:33, 25 October 2023) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2e1y.png|left|200px]]
 
-
<!--
+
==Crystal structure of propionate kinase (TdcD) from Salmonella typhimurium==
-
The line below this paragraph, containing "STRUCTURE_2e1y", creates the "Structure Box" on the page.
+
<StructureSection load='2e1y' size='340' side='right'caption='[[2e1y]], [[Resolution|resolution]] 2.60&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'>[[2e1y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E1Y 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]] 2.6&#8491;</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=2e1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e1y OCA], [https://pdbe.org/2e1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e1y RCSB], [https://www.ebi.ac.uk/pdbsum/2e1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e1y ProSAT]</span></td></tr>
-
{{STRUCTURE_2e1y| PDB=2e1y | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]
 +
== 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/e1/2e1y_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=2e1y ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Propionate kinase catalyses the last step in the anaerobic breakdown of L-threonine to propionate in which propionyl phosphate and ADP are converted to propionate and ATP. Here we report the structures of propionate kinase (TdcD) in the native form as well as in complex with diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) by X-ray crystallography. Structure of TdcD obtained after cocrystallization with ATP showed Ap4A bound to the active site pocket suggesting the presence of Ap4A synthetic activity in TdcD. Binding of Ap4A to the enzyme was confirmed by the structure determination of a TdcD-Ap4A complex obtained after cocrystallization of TdcD with commercially available Ap4A. Mass spectroscopic studies provided further evidence for the formation of Ap4A by propionate kinase in the presence of ATP. In the TdcD-Ap4A complex structure, Ap4A is present in an extended conformation with one adenosine moiety present in the nucleotide binding site and other in the proposed propionate binding site. These observations tend to support direct in-line transfer of phosphoryl group during the kinase reaction.
-
===Crystal structure of propionate kinase (TdcD) from Salmonella typhimurium===
+
Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity.,Simanshu DK, Savithri HS, Murthy MR Proteins. 2008 Mar;70(4):1379-88. PMID:17894350<ref>PMID:17894350</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_17894350}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2e1y" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 17894350 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_17894350}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
2E1Y is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E1Y OCA].
+
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-
 
+
[[Category: Murthy MRN]]
-
==Reference==
+
[[Category: Savithri HS]]
-
<ref group="xtra">PMID:17894350</ref><ref group="xtra">PMID:16139298</ref><ref group="xtra">PMID:16508089</ref><references group="xtra"/>
+
[[Category: Simanshu DK]]
-
[[Category: Propionate kinase]]
+
-
[[Category: Salmonella typhimurium]]
+
-
[[Category: Murthy, M R.N.]]
+
-
[[Category: Savithri, H S.]]
+
-
[[Category: Simanshu, D K.]]
+
-
[[Category: Acetate kinase]]
+
-
[[Category: Adp]]
+
-
[[Category: Amppnp]]
+
-
[[Category: Ap4a]]
+
-
[[Category: Atp]]
+
-
[[Category: Native]]
+
-
[[Category: Nucleotide]]
+
-
[[Category: Propionate kinase]]
+
-
[[Category: Tdcd]]
+
-
[[Category: Transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:44:46 2009''
+

Current revision

Crystal structure of propionate kinase (TdcD) from Salmonella typhimurium

PDB ID 2e1y

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/2e1y"
Personal tools