2dws
From Proteopedia
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|PDB= 2dws |SIZE=350|CAPTION= <scene name='initialview01'>2dws</scene>, resolution 1.85Å | |PDB= 2dws |SIZE=350|CAPTION= <scene name='initialview01'>2dws</scene>, resolution 1.85Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene> | + | |LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 Rhodobacter sphaeroides]) | |GENE= nirK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 Rhodobacter sphaeroides]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1zv2|1ZV2]], [[2dwt|2DWT]], [[2dy2|2DY2]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [http://www.ebi.ac.uk/pdbsum/2dws PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB]</span> | ||
}} | }} | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Jacobson, F.]] | [[Category: Jacobson, F.]] | ||
| - | [[Category: CU]] | ||
| - | [[Category: NO2]] | ||
[[Category: copper protein]] | [[Category: copper protein]] | ||
[[Category: cupredoxin]] | [[Category: cupredoxin]] | ||
[[Category: denitrification]] | [[Category: denitrification]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:40:37 2008'' |
Revision as of 23:40, 30 March 2008
| |||||||
| , resolution 1.85Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | nirK (Rhodobacter sphaeroides) | ||||||
| Activity: | Nitrite reductase (NO-forming), with EC number 1.7.2.1 | ||||||
| Related: | 1ZV2, 2DWT, 2DY2
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Cu-containing nitrite reductase at pH 8.4 with bound nitrite
Overview
Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.
About this Structure
2DWS is a Single protein structure of sequence from Rhodobacter sphaeroides. Full crystallographic information is available from OCA.
Reference
pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase., Jacobson F, Pistorius A, Farkas D, De Grip W, Hansson O, Sjolin L, Neutze R, J Biol Chem. 2007 Mar 2;282(9):6347-55. Epub 2006 Dec 5. PMID:17148448
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