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.


3t01

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:13, 14 March 2024) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoformate==
==Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoformate==
-
<StructureSection load='3t01' size='340' side='right' caption='[[3t01]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+
<StructureSection load='3t01' size='340' side='right'caption='[[3t01]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3t01]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sinorhizobium_meliloti Sinorhizobium meliloti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T01 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T01 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3t01]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinorhizobium_meliloti_1021 Sinorhizobium meliloti 1021]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T01 FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPF:PHOSPHONOFORMIC+ACID'>PPF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3szy|3szy]], [[3szz|3szz]], [[3t00|3t00]], [[3t02|3t02]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PPF:PHOSPHONOFORMIC+ACID'>PPF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phnA, RB0978, SM_b21538 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=382 Sinorhizobium meliloti])</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=3t01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t01 OCA], [https://pdbe.org/3t01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t01 RCSB], [https://www.ebi.ac.uk/pdbsum/3t01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t01 ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></td></tr>
+
</table>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t01 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3t01 RCSB], [http://www.ebi.ac.uk/pdbsum/3t01 PDBsum]</span></td></tr>
+
== Function ==
-
<table>
+
[https://www.uniprot.org/uniprot/Q92UV8_RHIME Q92UV8_RHIME]
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 A resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformate inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.
+
-
 
+
-
Structural and mechanistic insights into C-p bond hydrolysis by phosphonoacetate hydrolase.,Agarwal V, Borisova SA, Metcalf WW, van der Donk WA, Nair SK Chem Biol. 2011 Oct 28;18(10):1230-40. PMID:22035792<ref>PMID:22035792</ref>
+
-
 
+
-
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Nucleotide diphosphatase]]
+
[[Category: Large Structures]]
-
[[Category: Sinorhizobium meliloti]]
+
[[Category: Sinorhizobium meliloti 1021]]
-
[[Category: Agarwal, V.]]
+
[[Category: Agarwal V]]
-
[[Category: Nair, S K.]]
+
[[Category: Nair SK]]
-
[[Category: Alkaline phosphatase superfamily]]
+
-
[[Category: Hydrolase-hydrolase inhibitor complex]]
+
-
[[Category: Inhibitor]]
+

Current revision

Crystal Structure of Phosphonoacetate hydrolase from Sinorhizobium meliloti 1021 in complex with Phosphonoformate

PDB ID 3t01

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/3t01"
Personal tools