2q2v: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:2q2v.gif|left|200px]] | [[Image:2q2v.gif|left|200px]] | ||
'''Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida''' | {{Structure | ||
|PDB= 2q2v |SIZE=350|CAPTION= <scene name='initialview01'>2q2v</scene>, resolution 1.900Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] | |||
|GENE= bdhA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida]) | |||
}} | |||
'''Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
2Q2V is a [ | 2Q2V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q2V OCA]. | ||
==Reference== | ==Reference== | ||
Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida., Paithankar KS, Feller C, Kuettner EB, Keim A, Grunow M, Strater N, FEBS J. 2007 Nov;274(21):5767-79. PMID:[http:// | Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida., Paithankar KS, Feller C, Kuettner EB, Keim A, Grunow M, Strater N, FEBS J. 2007 Nov;274(21):5767-79. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17958702 17958702] | ||
[[Category: 3-hydroxybutyrate dehydrogenase]] | [[Category: 3-hydroxybutyrate dehydrogenase]] | ||
[[Category: Pseudomonas putida]] | [[Category: Pseudomonas putida]] | ||
| Line 26: | Line 35: | ||
[[Category: sdr]] | [[Category: sdr]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:20:53 2008'' | ||
Revision as of 19:20, 20 March 2008
| |||||||
| , resolution 1.900Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | bdhA (Pseudomonas putida) | ||||||
| Activity: | 3-hydroxybutyrate dehydrogenase, with EC number 1.1.1.30 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida
OverviewOverview
D-3-Hydroxybutyrate dehydrogenase from Pseudomonas putida belongs to the family of short-chain dehydrogenases/reductases. We have determined X-ray structures of the D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida, which was recombinantly expressed in Escherichia coli, in three different crystal forms to resolutions between 1.9 and 2.1 A. The so-called substrate-binding loop (residues 187-210) was partially disordered in several subunits, in both the presence and absence of NAD(+). However, in two subunits, this loop was completely defined in an open conformation in the apoenzyme and in a closed conformation in the complex structure with NAD(+). Structural comparisons indicated that the loop moves as a rigid body by about 46 degrees . However, the two small alpha-helices (alphaFG1 and alphaFG2) of the loop also re-orientated slightly during the conformational change. Probably, the interactions of Val185, Thr187 and Leu189 with the cosubstrate induced the conformational change. A model of the binding mode of the substrate D-3-hydroxybutyrate indicated that the loop in the closed conformation, as a result of NAD(+) binding, is positioned competent for catalysis. Gln193 is the only residue of the substrate-binding loop that interacts directly with the substrate. A translation, libration and screw (TLS) analysis of the rigid body movement of the loop in the crystal showed significant librational displacements, describing the coordinated movement of the substrate-binding loop in the crystal. NAD(+) binding increased the flexibility of the substrate-binding loop and shifted the equilibrium between the open and closed forms towards the closed form. The finding that all NAD(+) -bound subunits are present in the closed form and all NAD(+) -free subunits in the open form indicates that the loop closure is induced by cosubstrate binding alone. This mechanism may contribute to the sequential binding of cosubstrate followed by substrate.
About this StructureAbout this Structure
2Q2V is a Single protein structure of sequence from Pseudomonas putida. Full crystallographic information is available from OCA.
ReferenceReference
Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida., Paithankar KS, Feller C, Kuettner EB, Keim A, Grunow M, Strater N, FEBS J. 2007 Nov;274(21):5767-79. PMID:17958702
Page seeded by OCA on Thu Mar 20 18:20:53 2008