1d6y: Difference between revisions

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{{Structure
==CRYSTAL STRUCTURE OF E. COLI COPPER-CONTAINING AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE AND COMPLEXED WITH NITRIC OXIDE.==
|PDB= 1d6y |SIZE=350|CAPTION= <scene name='initialview01'>1d6y</scene>, resolution 2.4&Aring;
<StructureSection load='1d6y' size='340' side='right'caption='[[1d6y]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HY1:PHENYLACETALDEHYDE'>HY1</scene>, <scene name='pdbligand=NO:NITROGEN+OXIDE'>NO</scene>, <scene name='pdbligand=PEA:2-PHENYLETHYLAMINE'>PEA</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
<table><tr><td colspan='2'>[[1d6y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D6Y FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Amine_oxidase_(copper-containing) Amine oxidase (copper-containing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.6 1.4.3.6]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HY1:PHENYLACETALDEHYDE'>HY1</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=PEA:2-PHENYLETHYLAMINE'>PEA</scene>, <scene name='pdbligand=TYQ:3-AMINO-6-HYDROXY-TYROSINE'>TYQ</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=1d6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d6y OCA], [https://pdbe.org/1d6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d6y RCSB], [https://www.ebi.ac.uk/pdbsum/1d6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d6y ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/AMO_ECOLI AMO_ECOLI] The enzyme prefers aromatic over aliphatic amines.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d6/1d6y_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d6y ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
X-ray crystal structures of three species related to the oxidative half of the reaction of the copper-containing quinoprotein amine oxidase from Escherichia coli have been determined. Crystals were freeze-trapped either anaerobically or aerobically after exposure to substrate, and structures were determined to resolutions between 2.1 and 2.4 angstroms. The oxidation state of the quinone cofactor was investigated by single-crystal spectrophotometry. The structures reveal the site of bound dioxygen and the proton transfer pathways involved in oxygen reduction. The quinone cofactor is regenerated from the iminoquinone intermediate by hydrolysis involving Asp383, the catalytic base in the reductive half-reaction. Product aldehyde inhibits the hydrolysis, making release of product the rate-determining step of the reaction in the crystal.


'''CRYSTAL STRUCTURE OF E. COLI COPPER-CONTAINING AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE AND COMPLEXED WITH NITRIC OXIDE.'''
Visualization of dioxygen bound to copper during enzyme catalysis.,Wilmot CM, Hajdu J, McPherson MJ, Knowles PF, Phillips SE Science. 1999 Nov 26;286(5445):1724-8. PMID:10576737<ref>PMID:10576737</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d6y" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
X-ray crystal structures of three species related to the oxidative half of the reaction of the copper-containing quinoprotein amine oxidase from Escherichia coli have been determined. Crystals were freeze-trapped either anaerobically or aerobically after exposure to substrate, and structures were determined to resolutions between 2.1 and 2.4 angstroms. The oxidation state of the quinone cofactor was investigated by single-crystal spectrophotometry. The structures reveal the site of bound dioxygen and the proton transfer pathways involved in oxygen reduction. The quinone cofactor is regenerated from the iminoquinone intermediate by hydrolysis involving Asp383, the catalytic base in the reductive half-reaction. Product aldehyde inhibits the hydrolysis, making release of product the rate-determining step of the reaction in the crystal.
*[[Copper amine oxidase 3D structures|Copper amine oxidase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1D6Y is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D6Y OCA].
__TOC__
 
</StructureSection>
==Reference==
Visualization of dioxygen bound to copper during enzyme catalysis., Wilmot CM, Hajdu J, McPherson MJ, Knowles PF, Phillips SE, Science. 1999 Nov 26;286(5445):1724-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10576737 10576737]
[[Category: Amine oxidase (copper-containing)]]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hajdu, J.]]
[[Category: Hajdu J]]
[[Category: Knowles, P F.]]
[[Category: Knowles PF]]
[[Category: McPherson, M J.]]
[[Category: McPherson MJ]]
[[Category: Phillips, S E.V.]]
[[Category: Phillips SEV]]
[[Category: Wilmot, C M.]]
[[Category: Wilmot CM]]
[[Category: CA]]
[[Category: CU]]
[[Category: GOL]]
[[Category: HY1]]
[[Category: NO]]
[[Category: PEA]]
[[Category: reaction intermediate mimic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:33:53 2008''

Latest revision as of 11:23, 6 November 2024

CRYSTAL STRUCTURE OF E. COLI COPPER-CONTAINING AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE AND COMPLEXED WITH NITRIC OXIDE.CRYSTAL STRUCTURE OF E. COLI COPPER-CONTAINING AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE AND COMPLEXED WITH NITRIC OXIDE.

Structural highlights

1d6y is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:, , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMO_ECOLI The enzyme prefers aromatic over aliphatic amines.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

X-ray crystal structures of three species related to the oxidative half of the reaction of the copper-containing quinoprotein amine oxidase from Escherichia coli have been determined. Crystals were freeze-trapped either anaerobically or aerobically after exposure to substrate, and structures were determined to resolutions between 2.1 and 2.4 angstroms. The oxidation state of the quinone cofactor was investigated by single-crystal spectrophotometry. The structures reveal the site of bound dioxygen and the proton transfer pathways involved in oxygen reduction. The quinone cofactor is regenerated from the iminoquinone intermediate by hydrolysis involving Asp383, the catalytic base in the reductive half-reaction. Product aldehyde inhibits the hydrolysis, making release of product the rate-determining step of the reaction in the crystal.

Visualization of dioxygen bound to copper during enzyme catalysis.,Wilmot CM, Hajdu J, McPherson MJ, Knowles PF, Phillips SE Science. 1999 Nov 26;286(5445):1724-8. PMID:10576737[1]

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

See Also

References

  1. ↑ Wilmot CM, Hajdu J, McPherson MJ, Knowles PF, Phillips SE. Visualization of dioxygen bound to copper during enzyme catalysis. Science. 1999 Nov 26;286(5445):1724-8. PMID:10576737

1d6y, resolution 2.40Å

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