2j57: Difference between revisions

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[[Image:2j57.png|left|200px]]


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==X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex with amicyanin.==
The line below this paragraph, containing "STRUCTURE_2j57", creates the "Structure Box" on the page.
<StructureSection load='2j57' size='340' side='right'caption='[[2j57]], [[Resolution|resolution]] 2.25&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'>[[2j57]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J57 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
-->
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TQQ:(S)-2-AMINO-3-(6,7-DIHYDRO-6-IMINO-7-OXO-1H-INDOL-3-YL)PROPANOIC+ACID'>TQQ</scene></td></tr>
{{STRUCTURE_2j57|  PDB=2j57  |  SCENE=  }}
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aac|1aac]], [[1aaj|1aaj]], [[1aan|1aan]], [[1bxa|1bxa]], [[1mda|1mda]], [[1mg2|1mg2]], [[1mg3|1mg3]], [[1sf3|1sf3]], [[1sf5|1sf5]], [[1sfd|1sfd]], [[1sfh|1sfh]], [[1t5k|1t5k]], [[2mta|2mta]], [[2rac|2rac]], [[2bbk|2bbk]], [[2j55|2j55]], [[2j56|2j56]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methylamine_dehydrogenase_(amicyanin) Methylamine dehydrogenase (amicyanin)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.9.1 1.4.9.1] </span></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=2j57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j57 OCA], [https://pdbe.org/2j57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j57 RCSB], [https://www.ebi.ac.uk/pdbsum/2j57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j57 ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/AMCY_PARDE AMCY_PARDE]] Primary acceptor of electrons from methylamine dehydrogenase. Passes those electrons on either a soluble cytochrome c or to pseudoazurin. [[https://www.uniprot.org/uniprot/DHML_PARDE DHML_PARDE]] Methylamine dehydrogenase carries out the oxidation of methylamine. Electrons are passed from methylamine dehydrogenase to amicyanin. [[https://www.uniprot.org/uniprot/DHMH_PARDE DHMH_PARDE]] Methylamine dehydrogenase carries out the oxidation of methylamine. Electrons are passed from methylamine dehydrogenase to amicyanin.
== 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/j5/2j57_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2j57 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
X-ray exposure during crystallographic data collection can result in unintended redox changes in proteins containing functionally important redox centers. In order to directly monitor X-ray-derived redox changes in trapped oxidative half-reaction intermediates of Paracoccus denitrificans methylamine dehydrogenase, a commercially available single-crystal UV/Vis microspectrophotometer was installed on-line at the BioCARS beamline 14-BM-C at the Advanced Photon Source, Argonne, USA. Monitoring the redox state of the intermediates during X-ray exposure permitted the creation of a general multi-crystal data collection strategy to generate true structures of each redox intermediate.


===X-RAY REDUCED PARACCOCUS DENITRIFICANS METHYLAMINE DEHYDROGENASE N-QUINOL IN COMPLEX WITH AMICYANIN.===
Tracking X-ray-derived redox changes in crystals of a methylamine dehydrogenase/amicyanin complex using single-crystal UV/Vis microspectrophotometry.,Pearson AR, Pahl R, Kovaleva EG, Davidson VL, Wilmot CM J Synchrotron Radiat. 2007 Jan;14(Pt 1):92-8. Epub 2006 Dec 15. PMID:17211075<ref>PMID:17211075</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2j57" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17211075}}, adds the Publication Abstract to the page
*[[Methylamine dehydrogenase|Methylamine dehydrogenase]]
(as it appears on PubMed at http://www.pubmed.gov), where 17211075 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17211075}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2J57 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J57 OCA].
 
==Reference==
Tracking X-ray-derived redox changes in crystals of a methylamine dehydrogenase/amicyanin complex using single-crystal UV/Vis microspectrophotometry., Pearson AR, Pahl R, Kovaleva EG, Davidson VL, Wilmot CM, J Synchrotron Radiat. 2007 Jan;14(Pt 1):92-8. Epub 2006 Dec 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17211075 17211075]
[[Category: Amine dehydrogenase]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
[[Category: Protein complex]]
[[Category: Davidson, V L]]
[[Category: Davidson, V.]]
[[Category: Pahl, R]]
[[Category: Pahl, R.]]
[[Category: Pearson, A R]]
[[Category: Pearson, A R.]]
[[Category: Wilmot, C M]]
[[Category: Wilmot, C M.]]
[[Category: Copper]]
[[Category: Electron transport]]
[[Category: Electron transport]]
[[Category: Metal-binding]]
[[Category: Metal-binding]]
[[Category: Methylamine dehydrogenase single crystal microspectrophoto]]
[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
[[Category: Periplasmic]]
[[Category: Periplasmic]]
[[Category: Transport]]
[[Category: Single crystal microspectrophotometry]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:20:13 2008''

Latest revision as of 11:01, 19 January 2022

X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex with amicyanin.X-ray reduced Paraccocus denitrificans methylamine dehydrogenase N- quinol in complex with amicyanin.

Structural highlights

2j57 is a 12 chain structure with sequence from Paracoccus denitrificans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Activity:Methylamine dehydrogenase (amicyanin), with EC number 1.4.9.1
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[AMCY_PARDE] Primary acceptor of electrons from methylamine dehydrogenase. Passes those electrons on either a soluble cytochrome c or to pseudoazurin. [DHML_PARDE] Methylamine dehydrogenase carries out the oxidation of methylamine. Electrons are passed from methylamine dehydrogenase to amicyanin. [DHMH_PARDE] Methylamine dehydrogenase carries out the oxidation of methylamine. Electrons are passed from methylamine dehydrogenase to amicyanin.

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 exposure during crystallographic data collection can result in unintended redox changes in proteins containing functionally important redox centers. In order to directly monitor X-ray-derived redox changes in trapped oxidative half-reaction intermediates of Paracoccus denitrificans methylamine dehydrogenase, a commercially available single-crystal UV/Vis microspectrophotometer was installed on-line at the BioCARS beamline 14-BM-C at the Advanced Photon Source, Argonne, USA. Monitoring the redox state of the intermediates during X-ray exposure permitted the creation of a general multi-crystal data collection strategy to generate true structures of each redox intermediate.

Tracking X-ray-derived redox changes in crystals of a methylamine dehydrogenase/amicyanin complex using single-crystal UV/Vis microspectrophotometry.,Pearson AR, Pahl R, Kovaleva EG, Davidson VL, Wilmot CM J Synchrotron Radiat. 2007 Jan;14(Pt 1):92-8. Epub 2006 Dec 15. PMID:17211075[1]

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

See Also

References

  1. ↑ Pearson AR, Pahl R, Kovaleva EG, Davidson VL, Wilmot CM. Tracking X-ray-derived redox changes in crystals of a methylamine dehydrogenase/amicyanin complex using single-crystal UV/Vis microspectrophotometry. J Synchrotron Radiat. 2007 Jan;14(Pt 1):92-8. Epub 2006 Dec 15. PMID:17211075 doi:10.1107/S0909049506051259

2j57, resolution 2.25Å

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