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3myr

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Current revision

Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state

Structural highlights

3myr is a 8 chain structure with sequence from Allochromatium vinosum. 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

D3RV29_ALLVD

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

The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 A resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino acid sequence identity is approximately 50%. The bimetallic [NiFe] active site is located in the large subunit of the heterodimer and possesses three diatomic non-protein ligands coordinated to the Fe (two CN(-) , one CO). Ni is bound to the protein backbone via four cysteine thiolates; two of them also bridge the two metals. One of the bridging cysteines (Cys64) exhibits a modified thiolate in part of the sample. A mono-oxo bridging ligand was assigned between the metal ions of the catalytic center. This is in contrast to a proposal for Desulfovibrio sp. hydrogenases that show a di-oxo species in this position for the Ni-A state. The additional metal site located in the large subunit appears to be a Mg(2+) ion. Three iron-sulfur clusters were found in the small subunit that forms the electron transfer chain connecting the catalytic site with the molecular surface. The calculated anomalous Fourier map indicates a distorted proximal iron-sulfur cluster in part of the crystals. This altered proximal cluster is supposed to be paramagnetic and is exchange coupled to the Ni(3+) ion and the medial [Fe(3)S(4)](+) cluster that are both EPR active (S=1/2 species). This finding of a modified proximal cluster in the [NiFe] hydrogenase might explain the observation of split EPR signals that are occasionally detected in the oxidized state of membrane-bound [NiFe] hydrogenases as from A. vinosum.

The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state).,Ogata H, Kellers P, Lubitz W J Mol Biol. 2010 Sep 17;402(2):428-44. Epub 2010 Jul 29. PMID:20673834^[1]

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

References

↑ Ogata H, Kellers P, Lubitz W. The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state). J Mol Biol. 2010 Sep 17;402(2):428-44. Epub 2010 Jul 29. PMID:20673834 doi:10.1016/j.jmb.2010.07.041

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/3myr"

Categories: Allochromatium vinosum | Large Structures | Kellers P | Lubitz W | Ogata H

@@ Line 1: / Line 1: @@
 ==Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state==
-<StructureSection load='3myr' size='340' side='right' caption='[[3myr]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='3myr' size='340' side='right'caption='[[3myr]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3myr]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Allochromatium_vinosum Allochromatium vinosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MYR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MYR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3myr]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Allochromatium_vinosum Allochromatium vinosum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MYR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <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]] 2.1&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hydrogenase_(acceptor) Hydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.99.6 1.12.99.6] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFV:NI-FE+OXIDIZED+ACTIVE+CENTER'>NFV</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=3myr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3myr OCA], [http://pdbe.org/3myr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3myr RCSB], [http://www.ebi.ac.uk/pdbsum/3myr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3myr ProSAT]</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=3myr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3myr OCA], [https://pdbe.org/3myr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3myr RCSB], [https://www.ebi.ac.uk/pdbsum/3myr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3myr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D3RV29_ALLVD D3RV29_ALLVD]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 34: @@
 </StructureSection>
 [[Category: Allochromatium vinosum]]
-[[Category: Kellers, P]]
+[[Category: Large Structures]]
-[[Category: Lubitz, W]]
+[[Category: Kellers P]]
-[[Category: Ogata, H]]
+[[Category: Lubitz W]]
-[[Category: Iron-sulfur cluster]]
+[[Category: Ogata H]]
-[[Category: Ni-a state]]
-[[Category: Oxidoreductase]]
-[[Category: Photosynthetic purple-sulfur bacterium]]

3myr

From Proteopedia

Current revision

Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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