6jnj

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form)

Structural highlights

6jnj is a 2 chain structure with sequence from Azospirillum brasilense. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARAA_AZOBR Catalyzes the NAD(P)(+)-dependent conversion of L-arabinose to L-arabino-gamma-lactone. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NADP(+) to NAD(+) as electron acceptor. Displays high catalytic efficiency for both L-arabinose and D-galactose in vitro. However, the enzyme appears to be involved in the metabolism of L-arabinose but not D-galactose in vivo. To a lesser extent, is also active on D-talose and D-xylose as substrates in vitro, but not with D-arabinose, D-glucose, D-ribose, L-xylose, L-mannose, L-lyxose, and D-fructose.^[1]

Publication Abstract from PubMed

In Azospirillum brasilense, a gram-negative nitrogen-fixing bacterium, l-arabinose is converted to alpha-ketoglutarate through a nonphosphorylative metabolic pathway. In the first step in the pathway, l-arabinose is oxidized to l-arabino-gamma-lactone by NAD(P)-dependent l-arabinose 1-dehydrogenase (AraDH) belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Here, we determined the crystal structures of apo- and NADP-bound AraDH at 1.5 and 2.2 A resolutions, respectively. A docking model of l-arabinose and NADP-bound AraDH and structure-based mutational analyses suggest that Lys91 or Asp169 serves as a catalytic base and that Glu147, His153, and Asn173 are responsible for substrate recognition. In particular, Asn173 may play a role in the discrimination between l-arabinose and d-xylose, the C4 epimer of l-arabinose.

Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase.,Watanabe Y, Iga C, Watanabe Y, Watanabe S FEBS Lett. 2019 May 6. doi: 10.1002/1873-3468.13424. PMID:31058311^[2]

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

References

↑ Watanabe S, Kodaki T, Makino K. Cloning, expression, and characterization of bacterial L-arabinose 1-dehydrogenase involved in an alternative pathway of L-arabinose metabolism. J Biol Chem. 2006 Feb 3;281(5):2612-23. Epub 2005 Dec 2. PMID:16326697 doi:http://dx.doi.org/M506477200
↑ Watanabe Y, Iga C, Watanabe Y, Watanabe S. Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase. FEBS Lett. 2019 May 6. doi: 10.1002/1873-3468.13424. PMID:31058311 doi:http://dx.doi.org/10.1002/1873-3468.13424

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/6jnj"

Categories: Azospirillum brasilense | Large Structures | Iga C | Watanabe S | Watanabe Y

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6jnj is ON HOLD
+==Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form)==
+<StructureSection load='6jnj' size='340' side='right'caption='[[6jnj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6jnj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Azospirillum_brasilense Azospirillum brasilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JNJ FirstGlance]. <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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnj OCA], [https://pdbe.org/6jnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jnj RCSB], [https://www.ebi.ac.uk/pdbsum/6jnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ARAA_AZOBR ARAA_AZOBR] Catalyzes the NAD(P)(+)-dependent conversion of L-arabinose to L-arabino-gamma-lactone. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NADP(+) to NAD(+) as electron acceptor. Displays high catalytic efficiency for both L-arabinose and D-galactose in vitro. However, the enzyme appears to be involved in the metabolism of L-arabinose but not D-galactose in vivo. To a lesser extent, is also active on D-talose and D-xylose as substrates in vitro, but not with D-arabinose, D-glucose, D-ribose, L-xylose, L-mannose, L-lyxose, and D-fructose.<ref>PMID:16326697</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In Azospirillum brasilense, a gram-negative nitrogen-fixing bacterium, l-arabinose is converted to alpha-ketoglutarate through a nonphosphorylative metabolic pathway. In the first step in the pathway, l-arabinose is oxidized to l-arabino-gamma-lactone by NAD(P)-dependent l-arabinose 1-dehydrogenase (AraDH) belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Here, we determined the crystal structures of apo- and NADP-bound AraDH at 1.5 and 2.2 A resolutions, respectively. A docking model of l-arabinose and NADP-bound AraDH and structure-based mutational analyses suggest that Lys91 or Asp169 serves as a catalytic base and that Glu147, His153, and Asn173 are responsible for substrate recognition. In particular, Asn173 may play a role in the discrimination between l-arabinose and d-xylose, the C4 epimer of l-arabinose.
-Authors:
+Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase.,Watanabe Y, Iga C, Watanabe Y, Watanabe S FEBS Lett. 2019 May 6. doi: 10.1002/1873-3468.13424. PMID:31058311<ref>PMID:31058311</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6jnj" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Azospirillum brasilense]]
+[[Category: Large Structures]]
+[[Category: Iga C]]
+[[Category: Watanabe S]]
+[[Category: Watanabe Y]]

6jnj

From Proteopedia

Current revision

Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (apo-form)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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