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2vni

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X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH 2P-AMP AT 2.37 ANGSTROMS RESOLUTION

Structural highlights

2vni is a 1 chain structure with sequence from Rhodobacter capsulatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.24Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FENR_RHOCA Transports electrons between flavodoxin or ferredoxin and NADPH.^[1] ^[2] ^[3]

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

Ferredoxin-NADP(H) reductases catalyse the reversible hydride/electron exchange between NADP(H) and ferredoxin/flavodoxin, comprising a structurally defined family of flavoenzymes with two distinct subclasses. Those present in Gram-negative bacteria (FPRs) display turnover numbers of 1-5 s(-1) while the homologues of cyanobacteria and plants (FNRs) developed a 100-fold activity increase. We investigated nucleotide interactions and hydride transfer in Rhodobacter capsulatus FPR comparing them to those reported for FNRs. NADP(H) binding proceeds as in FNRs with stacking of the nicotinamide on the flavin, which resulted in formation of charge-transfer complexes prior to hydride exchange. The affinity of FPR for both NADP(H) and 2'-P-AMP was 100-fold lower than that of FNRs. The crystal structure of FPR in complex with 2'-P-AMP and NADP(+) allowed modelling of the adenosine ring system bound to the protein, whereas the nicotinamide portion was either not visible or protruding toward solvent in different obtained crystals. Stabilising contacts with the active site residues are different in the two reductase classes. We conclude that evolution to higher activities in FNRs was partially favoured by modification of NADP(H) binding in the initial complexes through changes in the active site residues involved in stabilisation of the adenosine portion of the nucleotide and in the mobile C-terminus of FPR.

Coenzyme binding and hydride transfer in Rhodobacter capsulatus ferredoxin/flavodoxin NADP(H) oxidoreductase.,Bortolotti A, Perez-Dorado I, Goni G, Medina M, Hermoso JA, Carrillo N, Cortez N Biochim Biophys Acta. 2009 Feb;1794(2):199-210. Epub 2008 Oct 7. PMID:18973834^[4]

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

References

↑ Bittel C, Tabares LC, Armesto M, Carrillo N, Cortez N. The oxidant-responsive diaphorase of Rhodobacter capsulatus is a ferredoxin (flavodoxin)-NADP(H) reductase. FEBS Lett. 2003 Oct 23;553(3):408-12. PMID:14572660
↑ Nogues I, Perez-Dorado I, Frago S, Bittel C, Mayhew SG, Gomez-Moreno C, Hermoso JA, Medina M, Cortez N, Carrillo N. The ferredoxin-NADP(H) reductase from Rhodobacter capsulatus: molecular structure and catalytic mechanism. Biochemistry. 2005 Sep 6;44(35):11730-40. PMID:16128574 doi:10.1021/bi0508183
↑ Bortolotti A, Sanchez-Azqueta A, Maya CM, Velazquez-Campoy A, Hermoso JA, Medina M, Cortez N. The C-terminal extension of bacterial flavodoxin-reductases: Involvement in the hydride transfer mechanism from the coenzyme. Biochim Biophys Acta. 2013 Sep 6;1837(1):33-43. doi:, 10.1016/j.bbabio.2013.08.008. PMID:24016470 doi:http://dx.doi.org/10.1016/j.bbabio.2013.08.008
↑ Bortolotti A, Perez-Dorado I, Goni G, Medina M, Hermoso JA, Carrillo N, Cortez N. Coenzyme binding and hydride transfer in Rhodobacter capsulatus ferredoxin/flavodoxin NADP(H) oxidoreductase. Biochim Biophys Acta. 2009 Feb;1794(2):199-210. Epub 2008 Oct 7. PMID:18973834 doi:10.1016/j.bbapap.2008.09.013

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/2vni"

Categories: Large Structures | Rhodobacter capsulatus | Hermoso JA | Perez-Dorado I

@@ Line 1: / Line 1: @@
 ==X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH 2P-AMP AT 2.37 ANGSTROMS RESOLUTION==
-<StructureSection load='2vni' size='340' side='right' caption='[[2vni]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
+<StructureSection load='2vni' size='340' side='right'caption='[[2vni]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vni]] is a 1 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=2VNI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VNI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vni]] is a 1 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=2VNI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VNI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2P:ADENOSINE-2-5-DIPHOSPHATE'>A2P</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</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]] 2.24&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2bgi|2bgi]], [[2bgj|2bgj]], [[2vnh|2vnh]], [[2vnj|2vnj]], [[2vnk|2vnk]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2P:ADENOSINE-2-5-DIPHOSPHATE'>A2P</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ferredoxin--NADP(+)_reductase Ferredoxin--NADP(+) reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.1.2 1.18.1.2] </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=2vni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vni OCA], [https://pdbe.org/2vni PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vni RCSB], [https://www.ebi.ac.uk/pdbsum/2vni PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vni 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=2vni FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vni OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vni RCSB], [http://www.ebi.ac.uk/pdbsum/2vni PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/FENR_RHOCA FENR_RHOCA] Transports electrons between flavodoxin or ferredoxin and NADPH.<ref>PMID:14572660</ref> <ref>PMID:16128574</ref> <ref>PMID:24016470</ref>
 == 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/vn/2vni_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vn/2vni_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/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=2vni ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vni" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Rhodobacter capsulatus]]
-[[Category: Hermoso, J A]]
+[[Category: Hermoso JA]]
-[[Category: Perez-Dorado, I]]
+[[Category: Perez-Dorado I]]
-[[Category: Electron transfer]]
-[[Category: Flavoprotein]]
-[[Category: Nadp]]
-[[Category: Oxidoreductase]]

2vni

From Proteopedia

Current revision

X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH 2P-AMP AT 2.37 ANGSTROMS RESOLUTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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