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.


3ndr

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (16:46, 1 November 2023) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti==
==Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti==
-
<StructureSection load='3ndr' size='340' side='right' caption='[[3ndr]], [[Resolution|resolution]] 2.88&Aring;' scene=''>
+
<StructureSection load='3ndr' size='340' side='right'caption='[[3ndr]], [[Resolution|resolution]] 2.88&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3ndr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700743 Atcc 700743]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NDR FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3ndr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NDR FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.88&#8491;</td></tr>
-
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mlr6807, pldh-t ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381 ATCC 700743])</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=3ndr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ndr OCA], [https://pdbe.org/3ndr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ndr RCSB], [https://www.ebi.ac.uk/pdbsum/3ndr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ndr 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/Pyridoxal_4-dehydrogenase Pyridoxal 4-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.107 1.1.1.107] </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=3ndr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ndr OCA], [http://pdbe.org/3ndr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ndr RCSB], [http://www.ebi.ac.uk/pdbsum/3ndr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ndr ProSAT]</span></td></tr>
+
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/PLDH_RHILO PLDH_RHILO]] Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Oxidizes pyridoxal to 4-pyridoxolactone, but does not have activity toward pyridoxal 5'-phosphate, pyridoxine, pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, pyridine, formaldehyde, 2-carboxybenzaldehyde or sugars.<ref>PMID:16824480</ref>
+
[https://www.uniprot.org/uniprot/PLDH_RHILO PLDH_RHILO] Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Oxidizes pyridoxal to 4-pyridoxolactone, but does not have activity toward pyridoxal 5'-phosphate, pyridoxine, pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, pyridine, formaldehyde, 2-carboxybenzaldehyde or sugars.<ref>PMID:16824480</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Pyridoxal 4-dehydrogenase from Mesorhizobium loti MAFF303099 was overexpressed in Escherichia coli. The recombinant selenomethionine-substituted enzyme was purified and crystallized by the sitting-drop vapour-diffusion method using PEG 4000 as precipitant. Crystals grew in the presence of 0.45 mM NAD(+). The crystals diffracted to 2.9 A resolution and belonged to the monoclinic space group P2(1), with unit-cell parameters a = 86.20, b = 51.11, c = 91.73 A, beta = 89.36 degrees. The calculated V(M) values suggested that the asymmetric unit contained four molecules.
+
-
 
+
-
Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti.,Chu HN, Kobayashi J, Yoshikane Y, Mikami B, Yagi T Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Jun 1;66(Pt, 6):718-20. Epub 2010 May 29. PMID:20516609<ref>PMID:20516609</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3ndr" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Atcc 700743]]
+
[[Category: Large Structures]]
-
[[Category: Pyridoxal 4-dehydrogenase]]
+
[[Category: Mesorhizobium loti]]
-
[[Category: Chu, H N]]
+
[[Category: Chu HN]]
-
[[Category: 4-pyridoxolactone]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Pyridoxal]]
+
-
[[Category: Short chain dehydrogenase/reductase]]
+
-
[[Category: Tpldh]]
+

Current revision

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

PDB ID 3ndr

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/3ndr"
Personal tools