1d7y: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1d7y" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d7y, resolution 2.1Å" /> '''CRYSTAL STRUCTURE OF ...
 
No edit summary
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1d7y.gif|left|200px]]<br /><applet load="1d7y" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1d7y, resolution 2.1&Aring;" />
'''CRYSTAL STRUCTURE OF NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4'''<br />


==Overview==
==CRYSTAL STRUCTURE OF NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4==
Oxidative biodegradation of aromatic compounds by bacteria usually begins, with hydroxylation of the aromatic ring by multi-component dioxygenases, like benzene dioxygenase, biphenyl dioxygenase, and others. These enzymes, are composed of ferredoxin reductase, ferredoxin, and terminal oxygenase., Reducing equivalents that originate from NADH are transferred from, ferredoxin reductase to ferredoxin and, in turn, to the terminal, oxygenase, thus resulting in the activation of a dioxygen. BphA4 is the, ferredoxin reductase component of biphenyl dioxygenase from Pseudomonas, sp. strain KKS102. The amino acid sequence of BphA4 exhibits significant, homology with the putidaredoxin reductase of the cytochrome P450cam system, in Pseudomonas putida, as well as with various other oxygenase-coupled, NADH-dependent ferredoxin reductases (ONFRs) of bacteria. To date, no, structural information has been provided for the ferredoxin reductase, component of the dioxygenase systems. In order to provide a structural, basis for discussing the mechanism of electron transport between, ferredoxin reductase and ferredoxin, crystal structures of BphA4 and its, NADH complex were solved. The three-dimensional structure of BphA4 is, different from those of ferredoxin reductases whose structures have, already been determined, but adopts essentially the same fold as the, enzymes of the glutathione reductase (GR) family. Also the, three-dimensional structure of the first two domains of BphA4 adopts a, fold similar to that of adrenodoxin reductase (AdR) in the mitochondrial, cytochrome P450 system. Comparing the amino acid sequence with what is, known of the three-dimensional structure of BphA4 strongly suggests that, the other ONFRs have secondary structural features that are similar to, that of BphA4. This analysis of the crystal structures of BphA4 suggests, that Lys53 and Glu159 seem to be involved in the hydride transfer from, NADH to FAD. Since the amino acid residues around the active site, some of, which seem to be important to electron transport, are highly conserved, among ONFRs, it is likely that the mechanism of electron transport of, BphA4 is quite applicable to other ONFRs.
<StructureSection load='1d7y' size='340' side='right'caption='[[1d7y]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1d7y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._KKS102 Pseudomonas sp. KKS102]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7Y FirstGlance]. <br>
1D7Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.] with FAD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D7Y OCA].
</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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7y OCA], [https://pdbe.org/1d7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7y RCSB], [https://www.ebi.ac.uk/pdbsum/1d7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7y ProSAT]</span></td></tr>
Crystal structure of NADH-dependent ferredoxin reductase component in biphenyl dioxygenase., Senda T, Yamada T, Sakurai N, Kubota M, Nishizaki T, Masai E, Fukuda M, Mitsuidagger Y, J Mol Biol. 2000 Dec 1;304(3):397-410. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11090282 11090282]
</table>
[[Category: Pseudomonas sp.]]
== Function ==
[[Category: Single protein]]
[https://www.uniprot.org/uniprot/Q52437_PSES1 Q52437_PSES1]
[[Category: Fukuda, M.]]
== Evolutionary Conservation ==
[[Category: Kubota, M.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Masai, E.]]
Check<jmol>
[[Category: Mitsui, Y.]]
  <jmolCheckbox>
[[Category: Nishizaki, T.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/1d7y_consurf.spt"</scriptWhenChecked>
[[Category: Sakurai, N.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Senda, T.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Yamada, T.]]
  </jmolCheckbox>
[[Category: FAD]]
</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=1d7y ConSurf].
[[Category: flavoprotein rossmann fold]]
<div style="clear:both"></div>
 
__TOC__
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:41:39 2007''
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas sp. KKS102]]
[[Category: Fukuda M]]
[[Category: Kubota M]]
[[Category: Masai E]]
[[Category: Mitsui Y]]
[[Category: Nishizaki T]]
[[Category: Sakurai N]]
[[Category: Senda T]]
[[Category: Yamada T]]

Latest revision as of 09:50, 7 February 2024

CRYSTAL STRUCTURE OF NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4CRYSTAL STRUCTURE OF NADH-DEPENDENT FERREDOXIN REDUCTASE, BPHA4

Structural highlights

1d7y is a 1 chain structure with sequence from Pseudomonas sp. KKS102. 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

Q52437_PSES1

Evolutionary Conservation

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

1d7y, resolution 2.10Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1d7y&oldid=4041645"