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| | ==Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark== | | ==Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark== |
| - | <StructureSection load='3aet' size='340' side='right' caption='[[3aet]], [[Resolution|resolution]] 2.91Å' scene=''> | + | <StructureSection load='3aet' size='340' side='right'caption='[[3aet]], [[Resolution|resolution]] 2.91Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3aet]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhodonostoc_capsulatum"_molisch_1907 "rhodonostoc capsulatum" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AET OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AET FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3aet]] 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=3AET OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AET FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.91Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3aek|3aek]], [[3aeq|3aeq]], [[3aer|3aer]], [[3aes|3aes]], [[3aeu|3aeu]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bchN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1061 "Rhodonostoc capsulatum" Molisch 1907]), bchB, bchK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1061 "Rhodonostoc capsulatum" Molisch 1907])</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=3aet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aet OCA], [https://pdbe.org/3aet PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3aet RCSB], [https://www.ebi.ac.uk/pdbsum/3aet PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3aet ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3aet FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aet OCA], [http://pdbe.org/3aet PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3aet RCSB], [http://www.ebi.ac.uk/pdbsum/3aet PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3aet ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> [[http://www.uniprot.org/uniprot/BCHB_RHOCB BCHB_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_00353]<ref>PMID:18358835</ref> | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ae/3aet_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ae/3aet_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Rhodonostoc capsulatum molisch 1907]] | + | [[Category: Large Structures]] |
| - | [[Category: Fujita, Y]] | + | [[Category: Rhodobacter capsulatus]] |
| - | [[Category: Kurisu, G]] | + | [[Category: Fujita Y]] |
| - | [[Category: Muraki, N]] | + | [[Category: Kurisu G]] |
| - | [[Category: Nomata, J]] | + | [[Category: Muraki N]] |
| - | [[Category: Shiba, T]] | + | [[Category: Nomata J]] |
| - | [[Category: Bacteriochlorophyll biosynthesis]]
| + | [[Category: Shiba T]] |
| - | [[Category: Chlorophyll biosynthesis]]
| + | |
| - | [[Category: Iron/sulfur cluster]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Photosynthesis]]
| + | |
| Structural highlights
Function
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][1]
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
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.
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nomata J, Ogawa T, Kitashima M, Inoue K, Fujita Y. NB-protein (BchN-BchB) of dark-operative protochlorophyllide reductase is the catalytic component containing oxygen-tolerant Fe-S clusters. FEBS Lett. 2008 Apr 16;582(9):1346-50. doi: 10.1016/j.febslet.2008.03.018. Epub, 2008 Mar 20. PMID:18358835 doi:http://dx.doi.org/10.1016/j.febslet.2008.03.018
- ↑ Muraki N, Nomata J, Ebata K, Mizoguchi T, Shiba T, Tamiaki H, Kurisu G, Fujita Y. X-ray crystal structure of the light-independent protochlorophyllide reductase. Nature. 2010 May 6;465(7294):110-4. PMID:20400946 doi:10.1038/nature08950
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