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.


5yo2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:24, 27 March 2024) (edit) (undo)
 
Line 1: Line 1:
==The crystal structure of Rv2747 from Mycobacterium tuberculosis in complex with Acetyl CoA and L-Arginine==
==The crystal structure of Rv2747 from Mycobacterium tuberculosis in complex with Acetyl CoA and L-Arginine==
-
<StructureSection load='5yo2' size='340' side='right' caption='[[5yo2]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+
<StructureSection load='5yo2' size='340' side='right'caption='[[5yo2]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5yo2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YO2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YO2 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5yo2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YO2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YO2 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.997&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rv2747 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Amino-acid_N-acetyltransferase Amino-acid N-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.1 2.3.1.1] </span></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=5yo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yo2 OCA], [https://pdbe.org/5yo2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yo2 RCSB], [https://www.ebi.ac.uk/pdbsum/5yo2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yo2 ProSAT]</span></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=5yo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yo2 OCA], [http://pdbe.org/5yo2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yo2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yo2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yo2 ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/ARGA_MYCTU ARGA_MYCTU]] Catalyzes the conversion of L-glutamate to alpha-N-acetyl-L-glutamate. L-glutamine is a significantly better substrate compared to L-glutamate.<ref>PMID:15838030</ref>
+
[https://www.uniprot.org/uniprot/ARGA_MYCTU ARGA_MYCTU] Catalyzes the conversion of L-glutamate to alpha-N-acetyl-L-glutamate. L-glutamine is a significantly better substrate compared to L-glutamate.<ref>PMID:15838030</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
The Mycobacterium tuberculosis (Mtb) Rv2747 gene encodes for a functional protein known as ArgA, which plays an important role in the first step of the l-arginine biosynthesis pathway. ArgA transfers the acetyl group from the acetyl-CoA to either l-glutamate or l-glutamine, which are the known substrates. Here, we present two crystal structures of ArgA: one complexed with CoA and product bound N-acetylglutamine and the other complexed with acetyl-CoA and the inhibitor l-arginine at 2.3 and 3.0A resolution respectively. The Mtb ArgA protomer was found to have a "V" cleft and a "beta" bulge, archetypal of a classical GCN5-related N-acetyltransferase superfamily of proteins. The product bound form implies that ArgA can also acetylate l-glutamine like l-glutamate. The active site is strongly inhibited by l-arginine resulting in a closed conformation of ArgA and both l-arginine and N-acetylglutamine were found to occupy at the same active site. Together with structural analysis, molecular docking studies, microscale thermophoresis and enzyme inhibition assays, we conclude that l-glutamine, l-glutamate and l-arginine, all occupy at the same active site of ArgA. Furthermore in case of Mtb ArgA, l-arginine does not act as an allosteric inhibitor unlike other N-acetylglutamate synthase family of proteins.
+
-
 
+
-
Structural insights into the substrate binding mechanism of novel ArgA from Mycobacterium tuberculosis.,Das U, Singh E, Dharavath S, Subhramanyam UKT, Pal RK, Vijayan R, Menon S, Kumar S, Gourinath S, Srinivasan A Int J Biol Macromol. 2018 Dec 18. pii: S0141-8130(18)35189-4. doi:, 10.1016/j.ijbiomac.2018.12.163. PMID:30576731<ref>PMID:30576731</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5yo2" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Amino-acid N-acetyltransferase]]
+
[[Category: Large Structures]]
-
[[Category: Myctu]]
+
[[Category: Mycobacterium tuberculosis H37Rv]]
-
[[Category: Das, U]]
+
[[Category: Das U]]
-
[[Category: Gourinath, S]]
+
[[Category: Gourinath S]]
-
[[Category: Pal, R K]]
+
[[Category: Pal RK]]
-
[[Category: Singh, E]]
+
[[Category: Singh E]]
-
[[Category: Srinivasan, A]]
+
[[Category: Srinivasan A]]
-
[[Category: Subhramanyam, U K.Tiruttani]]
+
[[Category: Tiruttani Subhramanyam UK]]
-
[[Category: Acetyltransferase]]
+
-
[[Category: Transferase]]
+

Current revision

The crystal structure of Rv2747 from Mycobacterium tuberculosis in complex with Acetyl CoA and L-Arginine

PDB ID 5yo2

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/5yo2"
Personal tools