3ndr

From Proteopedia

(Difference between revisions)

Revision as of 13:04, 16 January 2019

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

Structural highlights

3ndr is a 4 chain structure with sequence from Atcc 700743. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	mlr6807, pldh-t (ATCC 700743)
Activity:	Pyridoxal 4-dehydrogenase, with EC number 1.1.1.107
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yokochi N, Nishimura S, Yoshikane Y, Ohnishi K, Yagi T. Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti. Arch Biochem Biophys. 2006 Aug 1;452(1):1-8. Epub 2006 Jun 16. PMID:16824480 doi:http://dx.doi.org/10.1016/j.abb.2006.06.002
↑ Chu HN, Kobayashi J, Yoshikane Y, Mikami B, Yagi T. Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Jun 1;66(Pt, 6):718-20. Epub 2010 May 29. PMID:20516609 doi:10.1107/S1744309110015101

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ndr"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ndr' size='340' side='right' caption='[[3ndr]], [[Resolution|resolution]] 2.88&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ndr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33669 Atcc 33669]. 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 [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>
 </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>
 <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='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 33669])</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='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>
@@ Line 25: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 33669]]
+[[Category: Atcc 700743]]
 [[Category: Pyridoxal 4-dehydrogenase]]
 [[Category: Chu, H N]]

3ndr

From Proteopedia

Revision as of 13:04, 16 January 2019

Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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