3rja

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue

Structural highlights

3rja is a 1 chain structure with sequence from Microdochium nivale. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MNCO_MICNN Catalyzes the selective oxidation of C1 hydroxyl moieties on mono-, oligo- and polysaccharides with concomitant reduction of molecular oxygen to hydrogen peroxide. This results in the formation of the corresponding lactones, which typically undergo spontaneous hydrolysis. Carbohydrate oxidase is able to oxidize a variety of substrates including D-glucose, D-galactose, D-xylose, D-maltose, D-cellobiose, and lactose. In addition, among various oligosaccharides, the enzyme preferred tetrameric dextrins, indicating a favorable interaction of four linked glucose units with the substrate binding pocket.^[1] [PROSITE-ProRule:PRU00718]^[2]

Publication Abstract from PubMed

Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66 A resolution, with unit-cell parameters a = b = 55.7, c = 610.4 A and apparent space group P6(2)22. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5 A, beta = 95.7 degrees . Data sets were collected to a resolution of 2.4 A. The structure was solved by the molecular-replacement method. Model refinement is currently in progress.

Crystallization of carbohydrate oxidase from Microdochium nivale.,Duskova J, Dohnalek J, Skalova T, Ostergaard LH, Fuglsang CC, Kolenko P, Stepankova A, Hasek J Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt 6):638-40., Epub 2009 May 23. PMID:019478452^[3]

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

References

↑ Xu F, Golightly EJ, Fuglsang CC, Schneider P, Duke KR, Lam L, Christensen S, Brown KM, Jørgensen CT, Brown SH. A novel carbohydrate:acceptor oxidoreductase from Microdochium nivale. Eur J Biochem. 2001 Feb;268(4):1136-42. PMID:11179980 doi:10.1046/j.1432-1327.2001.01982.x
↑ Xu F, Golightly EJ, Fuglsang CC, Schneider P, Duke KR, Lam L, Christensen S, Brown KM, Jørgensen CT, Brown SH. A novel carbohydrate:acceptor oxidoreductase from Microdochium nivale. Eur J Biochem. 2001 Feb;268(4):1136-42. PMID:11179980 doi:10.1046/j.1432-1327.2001.01982.x
↑ Duskova J, Dohnalek J, Skalova T, Ostergaard LH, Fuglsang CC, Kolenko P, Stepankova A, Hasek J. Crystallization of carbohydrate oxidase from Microdochium nivale. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt 6):638-40., Epub 2009 May 23. PMID:19478452 doi:10.1107/S1744309109017643

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/3rja"

@@ Line 1: / Line 1: @@
-[[Image:3rja.jpg|left|200px]]
-<!--
+==Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue==
-The line below this paragraph, containing "STRUCTURE_3rja", creates the "Structure Box" on the page.
+<StructureSection load='3rja' size='340' side='right'caption='[[3rja]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3rja]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RJA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABL:(2R,3R,4R,5R)-4,5-DIHYDROXY-2-(HYDROXYMETHYL)-6-OXOPIPERIDIN-3-YL+BETA-D-GLUCOPYRANOSIDE'>ABL</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3rja|  PDB=3rja  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rja OCA], [https://pdbe.org/3rja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rja RCSB], [https://www.ebi.ac.uk/pdbsum/3rja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rja ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MNCO_MICNN MNCO_MICNN] Catalyzes the selective oxidation of C1 hydroxyl moieties on mono-, oligo- and polysaccharides with concomitant reduction of molecular oxygen to hydrogen peroxide. This results in the formation of the corresponding lactones, which typically undergo spontaneous hydrolysis. Carbohydrate oxidase is able to oxidize a variety of substrates including D-glucose, D-galactose, D-xylose, D-maltose, D-cellobiose, and lactose. In addition, among various oligosaccharides, the enzyme preferred tetrameric dextrins, indicating a favorable interaction of four linked glucose units with the substrate binding pocket.<ref>PMID:11179980</ref> [PROSITE-ProRule:PRU00718]<ref>PMID:11179980</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66 A resolution, with unit-cell parameters a = b = 55.7, c = 610.4 A and apparent space group P6(2)22. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5 A, beta = 95.7 degrees . Data sets were collected to a resolution of 2.4 A. The structure was solved by the molecular-replacement method. Model refinement is currently in progress.
-===Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue===
+Crystallization of carbohydrate oxidase from Microdochium nivale.,Duskova J, Dohnalek J, Skalova T, Ostergaard LH, Fuglsang CC, Kolenko P, Stepankova A, Hasek J Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt 6):638-40., Epub 2009 May 23. PMID:019478452<ref>PMID:019478452</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19478452}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3rja" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19478452 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19478452}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3rja]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJA OCA].
-==Reference==
-<ref group="xtra">PMID:019478452</ref><references group="xtra"/>
-[[Category: Glucose oxidase]]
 [[Category: Microdochium nivale]]
-[[Category: Dohnalek, J.]]
+[[Category: Dohnalek J]]
-[[Category: Duskova, J.]]
+[[Category: Duskova J]]
-[[Category: Fuglsang, C C.]]
+[[Category: Fuglsang CC]]
-[[Category: Hasek, J.]]
+[[Category: Hasek J]]
-[[Category: Kolenko, P.]]
+[[Category: Kolenko P]]
-[[Category: Koval, T.]]
+[[Category: Koval T]]
-[[Category: Ostergaard, L H.]]
+[[Category: Ostergaard LH]]
-[[Category: Skalova, T.]]
+[[Category: Skalova T]]
-[[Category: Stepankova, A.]]
+[[Category: Stepankova A]]
-[[Category: Berberine and berberine-like domain]]
-[[Category: Carbohydrate/sugar binding]]
-[[Category: Extracellular]]
-[[Category: Fad binding]]
-[[Category: Fad binding domain]]
-[[Category: Glucooligosaccharide oxidase]]
-[[Category: Oxidoreductase]]
-[[Category: Protein-substrate analogue complex]]

3rja

From Proteopedia

Current revision

Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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