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3aek

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[[Image:3aek.png|left|200px]]
 
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==Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark==
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The line below this paragraph, containing "STRUCTURE_3aek", creates the "Structure Box" on the page.
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<StructureSection load='3aek' size='340' side='right'caption='[[3aek]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3aek]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AEK FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PMR:PROTOCHLOROPHYLLIDE'>PMR</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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{{STRUCTURE_3aek| PDB=3aek | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3aek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aek OCA], [https://pdbe.org/3aek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aek RCSB], [https://www.ebi.ac.uk/pdbsum/3aek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aek ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BCHN_RHOCB BCHN_RHOCB] Component of the dark-operative protochlorophyllide reductase (DPOR) that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide). This reaction is light-independent. The NB-protein (BchN-BchB) is the catalytic component of the complex.[HAMAP-Rule:MF_00352]<ref>PMID:18358835</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ae/3aek_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3aek ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Photosynthetic organisms adopt two different strategies for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide) to form chlorophyllide a, the direct precursor of chlorophyll a (refs 1-4). The first involves the activity of the light-dependent Pchlide oxidoreductase, and the second involves the light-independent (dark-operative) Pchlide oxidoreductase (DPOR). DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer), which are structurally related to nitrogenase Fe protein and MoFe protein, respectively. Here we report the crystal structure of the NB-protein of DPOR from Rhodobacter capsulatus at a resolution of 2.3A. As expected, the overall structure is similar to that of nitrogenase MoFe protein: each catalytic BchN-BchB unit contains one Pchlide and one iron-sulphur cluster (NB-cluster) coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific Pchlide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit. We propose a unique trans-specific reduction mechanism in which the distorted C17-propionate of Pchlide and an aspartate from BchB serve as proton donors for C18 and C17 of Pchlide, respectively. Intriguingly, the spatial arrangement of the NB-cluster and Pchlide is almost identical to that of the P-cluster and FeMo-cofactor in nitrogenase MoFe-protein, illustrating that a common architecture exists to reduce chemically stable multibonds of porphyrin and dinitrogen.
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===Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark===
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X-ray crystal structure of the light-independent protochlorophyllide reductase.,Muraki N, Nomata J, Ebata K, Mizoguchi T, Shiba T, Tamiaki H, Kurisu G, Fujita Y Nature. 2010 May 6;465(7294):110-4. PMID:20400946<ref>PMID:20400946</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_20400946}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3aek" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20400946 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20400946}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[3aek]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AEK OCA].
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==Reference==
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<ref group="xtra">PMID:20400946</ref><references group="xtra"/>
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[[Category: Rhodobacter capsulatus]]
[[Category: Rhodobacter capsulatus]]
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[[Category: Fujita, Y.]]
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[[Category: Fujita Y]]
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[[Category: Kurisu, G.]]
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[[Category: Kurisu G]]
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[[Category: Muraki, N.]]
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[[Category: Muraki N]]
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[[Category: Nomata, J.]]
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[[Category: Nomata J]]
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[[Category: Shiba, T.]]
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[[Category: Shiba T]]
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[[Category: Bacteriochlorophyll biosynthesis]]
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[[Category: Chlorophyll biosynthesis]]
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[[Category: Iron/sulfur cluster]]
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[[Category: Oxidoreductase]]
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[[Category: Photosynthesis]]
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Current revision

Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark

PDB ID 3aek

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