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.


4bvj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 3: Line 3:
<StructureSection load='4bvj' size='340' side='right'caption='[[4bvj]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='4bvj' size='340' side='right'caption='[[4bvj]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4bvj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17989 Atcc 17989]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BVJ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4bvj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paucimonas_lemoignei Paucimonas lemoignei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BVJ FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4btv|4btv]], [[4bvk|4bvk]], [[4bvl|4bvl]]</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=4bvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bvj OCA], [https://pdbe.org/4bvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bvj RCSB], [https://www.ebi.ac.uk/pdbsum/4bvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bvj ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(3-hydroxybutyrate)_depolymerase Poly(3-hydroxybutyrate) depolymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.75 3.1.1.75] </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=4bvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bvj OCA], [http://pdbe.org/4bvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bvj RCSB], [http://www.ebi.ac.uk/pdbsum/4bvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bvj ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[[https://www.uniprot.org/uniprot/Q939Q9_PAULE Q939Q9_PAULE]]
-
Five amino acids (Y105, Y176, Y189, Y189, W207) that constitute the substrate binding site of PHB depolymerase PhaZ7 were identified. All residues are located at a single surface-exposed location of PhaZ7. Exchange of these amino acids by less hydrophobic, hydrophilic or negatively charged residues reduced binding of PhaZ7 to PHB. Modifications of other residues at the PhaZ7 surface (F9, Y66, Y103, Y124, Y169, Y172, Y173, F198, Y203, Y204, F251, W252) had no effect on substrate binding. The PhaZ7 wild type protein, three muteins with single amino acid exchanges (Y105A, Y105E, Y190E), a PhaZ7 variant with deletion of residues 202-208, and PhaZ7 in which the active site serine had been replaced by alanine (S136A) were crystallized and their structures were determined at 1.6 to 2.0 A resolution. The structures were almost identical but revealed flexibility of some regions. Structural analysis of PhaZ7 (S136A) with bound 3-hydroxybutyrate tetramer showed that the substrate binds in a cleft that is composed of Y105, Y176, Y189 and Y190 and thus confirmed the data obtained by site-directed mutagenesis. To the best of our knowledge this is the first example in which the substrate binding site of a PHB depolymerase is documented at a molecular and structural level.
+
-
 
+
-
Biochemical Analysis and Structure Determination of Paucimonas lemoignei Poly(3-hydroxybutyrate) (PHB) Depolymerase PhaZ7 Muteins Reveal the PHB Binding Site and Details of Substrate-Enzyme Interactions.,Jendrossek D, Hermawan S, Subedi B, Papageorgiou AC Mol Microbiol. 2013 Sep 5. doi: 10.1111/mmi.12391. PMID:24007310<ref>PMID:24007310</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4bvj" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 17989]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Hermawan, S]]
+
[[Category: Paucimonas lemoignei]]
-
[[Category: Jendrossek, D]]
+
[[Category: Hermawan S]]
-
[[Category: Papageorgiou, A C]]
+
[[Category: Jendrossek D]]
-
[[Category: Subedi, B]]
+
[[Category: Papageorgiou AC]]
-
[[Category: Biopolymer binding]]
+
[[Category: Subedi B]]
-
[[Category: Catalytic triad]]
+
-
[[Category: Hydrolase]]
+

Revision as of 17:11, 7 September 2022

Structure of Y105A mutant of PhaZ7 PHB depolymerase

PDB ID 4bvj

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/4bvj"
Personal tools