1h2a

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1h2a.jpg|left|200px]]<br /><applet load="1h2a" size="350" color="white" frame="true" align="right" spinBox="true"
+
[[Image:1h2a.jpg|left|200px]]
-
caption="1h2a, resolution 1.8&Aring;" />
+
 
-
'''SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS'''<br />
+
{{Structure
 +
|PDB= 1h2a |SIZE=350|CAPTION= <scene name='initialview01'>1h2a</scene>, resolution 1.8&Aring;
 +
|SITE=
 +
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene> and <scene name='pdbligand=NFE:NI-FE ACTIVE CENTER'>NFE</scene>
 +
|ACTIVITY= [http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2]
 +
|GENE=
 +
}}
 +
 
 +
'''SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS'''
 +
 
==Overview==
==Overview==
Line 7: Line 16:
==About this Structure==
==About this Structure==
-
1H2A is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SF4:'>SF4</scene>, <scene name='pdbligand=F3S:'>F3S</scene> and <scene name='pdbligand=NFE:'>NFE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Ferredoxin_hydrogenase Ferredoxin hydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.12.7.2 1.12.7.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H2A OCA].
+
1H2A is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H2A OCA].
==Reference==
==Reference==
-
Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis., Higuchi Y, Yagi T, Yasuoka N, Structure. 1997 Dec 15;5(12):1671-80. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9438867 9438867]
+
Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis., Higuchi Y, Yagi T, Yasuoka N, Structure. 1997 Dec 15;5(12):1671-80. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9438867 9438867]
[[Category: Desulfovibrio vulgaris]]
[[Category: Desulfovibrio vulgaris]]
[[Category: Ferredoxin hydrogenase]]
[[Category: Ferredoxin hydrogenase]]
Line 28: Line 37:
[[Category: so ligand]]
[[Category: so ligand]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:56:33 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:31:11 2008''

Revision as of 09:31, 20 March 2008

Image:1h2a.jpg


PDB ID 1h2a

Drag the structure with the mouse to rotate
, resolution 1.8Å
Ligands: , , and
Activity: Ferredoxin hydrogenase, with EC number 1.12.7.2
Coordinates: save as pdb, mmCIF, xml



SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS


Overview

BACKGROUND: The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase. RESULTS: The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center. CONCLUSIONS: From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.

About this Structure

1H2A is a Protein complex structure of sequences from Desulfovibrio vulgaris. Full crystallographic information is available from OCA.

Reference

Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis., Higuchi Y, Yagi T, Yasuoka N, Structure. 1997 Dec 15;5(12):1671-80. PMID:9438867

Page seeded by OCA on Thu Mar 20 11:31:11 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1h2a"
Personal tools