1ndt
From Proteopedia
(New page: 200px<br /><applet load="1ndt" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ndt, resolution 2.10Å" /> '''NITRITE REDUCTASE FR...) |
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| - | [[Image:1ndt.jpg|left|200px]]<br /><applet load="1ndt" size=" | + | [[Image:1ndt.jpg|left|200px]]<br /><applet load="1ndt" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1ndt, resolution 2.10Å" /> | caption="1ndt, resolution 2.10Å" /> | ||
'''NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS'''<br /> | '''NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Denitrification is one of the main steps of the global nitrogen cycle that | + | Denitrification is one of the main steps of the global nitrogen cycle that is sustained by prokaryotic organisms. Denitrifying bacteria use two entirely different enzymes in this process, one based on haem cd1 prosthetic groups and the other on type 1-type 2 Cu centres. Copper-containing nitrite reductases (NiRs) are sub-divided into blue and green NiRs, which are respectively thought to be redox partners of azurins and pseudo-azurins. Crystallographic structures of the blue nitrite reductase from Alcaligenes xylosoxidans (AxNiR) are presented in the oxidised hexagonal form and the substrate-bound orthorhombic form to 2.1 A and 2.8 A resolution, respectively. The complete amino acid sequence of AxNiR has been determined by conventional chemical analysis. A 3 A structure of AxNiR has been published where the modelling was based on the sequence of another blue NiR. The higher resolution of the hexagonal form together with the correct sequence allows a detailed comparison with the crystallographic structures of the green NiRs. There is a striking difference in the overall surface charge distribution between the two sub-groups, providing a neat structural explanation for their different reactivities to pseudoazurin or azurin and supporting the view that electron transfer proceeds via complex formation. A detailed examination of the type-1 Cu site, the site responsible for the colour, reveals several subtle differences, including a lateral displacement of 0.7 A for Smet. The structure of the type-2 Cu site, and changes that occur upon substrate binding are discussed in terms of the catalytic mechanism. The similarity of the type 2 Cu site to the catalytic Zn site in carbonic anhydrase and the catalytic Cu site of superoxide dismutase is re-examined in view of the high-resolution (2.1 A) structure. |
==About this Structure== | ==About this Structure== | ||
| - | 1NDT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans] with CU and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] Full crystallographic information is available from [http:// | + | 1NDT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans] with <scene name='pdbligand=CU:'>CU</scene> and <scene name='pdbligand=CL:'>CL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDT OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Nitrite reductase (NO-forming)]] | [[Category: Nitrite reductase (NO-forming)]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Dodd, F | + | [[Category: Dodd, F E.]] |
| - | [[Category: Eady, R | + | [[Category: Eady, R R.]] |
| - | [[Category: Hasnain, S | + | [[Category: Hasnain, S S.]] |
[[Category: Vanbeeumen, J.]] | [[Category: Vanbeeumen, J.]] | ||
[[Category: CL]] | [[Category: CL]] | ||
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[[Category: nitrite reductase]] | [[Category: nitrite reductase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:05:03 2008'' |
Revision as of 12:05, 21 February 2008
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NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
Overview
Denitrification is one of the main steps of the global nitrogen cycle that is sustained by prokaryotic organisms. Denitrifying bacteria use two entirely different enzymes in this process, one based on haem cd1 prosthetic groups and the other on type 1-type 2 Cu centres. Copper-containing nitrite reductases (NiRs) are sub-divided into blue and green NiRs, which are respectively thought to be redox partners of azurins and pseudo-azurins. Crystallographic structures of the blue nitrite reductase from Alcaligenes xylosoxidans (AxNiR) are presented in the oxidised hexagonal form and the substrate-bound orthorhombic form to 2.1 A and 2.8 A resolution, respectively. The complete amino acid sequence of AxNiR has been determined by conventional chemical analysis. A 3 A structure of AxNiR has been published where the modelling was based on the sequence of another blue NiR. The higher resolution of the hexagonal form together with the correct sequence allows a detailed comparison with the crystallographic structures of the green NiRs. There is a striking difference in the overall surface charge distribution between the two sub-groups, providing a neat structural explanation for their different reactivities to pseudoazurin or azurin and supporting the view that electron transfer proceeds via complex formation. A detailed examination of the type-1 Cu site, the site responsible for the colour, reveals several subtle differences, including a lateral displacement of 0.7 A for Smet. The structure of the type-2 Cu site, and changes that occur upon substrate binding are discussed in terms of the catalytic mechanism. The similarity of the type 2 Cu site to the catalytic Zn site in carbonic anhydrase and the catalytic Cu site of superoxide dismutase is re-examined in view of the high-resolution (2.1 A) structure.
About this Structure
1NDT is a Single protein structure of sequence from Achromobacter xylosoxidans with and as ligands. Active as Nitrite reductase (NO-forming), with EC number 1.7.2.1 Full crystallographic information is available from OCA.
Reference
X-ray structure of a blue-copper nitrite reductase in two crystal forms. The nature of the copper sites, mode of substrate binding and recognition by redox partner., Dodd FE, Van Beeumen J, Eady RR, Hasnain SS, J Mol Biol. 1998 Sep 18;282(2):369-82. PMID:9735294
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