3aer

From Proteopedia

(Difference between revisions)

Revision as of 12:30, 4 August 2016

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

Structural highlights

3aer is a 4 chain structure with sequence from "rhodonostoc_capsulatum"_molisch_1907 "rhodonostoc capsulatum" molisch 1907. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	3aek, 3aeq, 3aes, 3aet, 3aeu
Gene:	bchN ("Rhodonostoc capsulatum" Molisch 1907), bchB, bchK ("Rhodonostoc capsulatum" Molisch 1907)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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] [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]^[2]

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^[3]

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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3aer"

@@ Line 1: / Line 1: @@
 ==Structure of the light-independent protochlorophyllide reductase catalyzing a key reduction for greening in the dark==
 <StructureSection load='3aer' size='340' side='right' caption='[[3aer]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3aer]] 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=3AER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AER FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3aer]] 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=3AER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AER 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>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3aek|3aek]], [[3aeq|3aeq]], [[3aes|3aes]], [[3aet|3aet]], [[3aeu|3aeu]]</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 Rhodobacter capsulatus]), bchB, bchK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1061 Rhodobacter capsulatus])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3aer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aer OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3aer RCSB], [http://www.ebi.ac.uk/pdbsum/3aer PDBsum]</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=3aer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3aer OCA], [http://pdbe.org/3aer PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3aer RCSB], [http://www.ebi.ac.uk/pdbsum/3aer PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3aer ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BCHN_RHOCA BCHN_RHOCA]] 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_RHOCA BCHB_RHOCA]] 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>
+[[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 18: / Line 19: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3aer ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3aer" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Rhodobacter capsulatus]]
+[[Category: Rhodonostoc capsulatum molisch 1907]]
 [[Category: Fujita, Y]]
 [[Category: Kurisu, G]]

3aer

From Proteopedia

Revision as of 12:30, 4 August 2016

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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