2dfv
From Proteopedia
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|PDB= 2dfv |SIZE=350|CAPTION= <scene name='initialview01'>2dfv</scene>, resolution 2.05Å | |PDB= 2dfv |SIZE=350|CAPTION= <scene name='initialview01'>2dfv</scene>, resolution 2.05Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/L-threonine_3-dehydrogenase L-threonine 3-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.103 1.1.1.103] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/L-threonine_3-dehydrogenase L-threonine 3-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.103 1.1.1.103] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dfv OCA], [http://www.ebi.ac.uk/pdbsum/2dfv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dfv RCSB]</span> | ||
}} | }} | ||
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[[Category: Nakagawa, A.]] | [[Category: Nakagawa, A.]] | ||
[[Category: Nakamura, T.]] | [[Category: Nakamura, T.]] | ||
| - | [[Category: NAD]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: ZN]] | ||
[[Category: alchol dehydrogenase]] | [[Category: alchol dehydrogenase]] | ||
[[Category: archaea]] | [[Category: archaea]] | ||
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[[Category: threonine dehydrogenase]] | [[Category: threonine dehydrogenase]] | ||
| - | ''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 02:34:09 2008'' |
Revision as of 23:34, 30 March 2008
| |||||||
| , resolution 2.05Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | L-threonine 3-dehydrogenase, with EC number 1.1.1.103 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Hyperthermophilic threonine dehydrogenase from Pyrococcus horikoshii
Overview
L-threonine dehydrogenase (TDH) is an enzyme that catalyzes the oxidation of L-threonine to 2-amino-3-ketobutyrate. We solved the first crystal structure of a medium chain L-threonine dehydrogenase from a hyperthermophilic archaeon, Pyrococcus horikoshii (PhTDH), by the single wavelength anomalous diffraction method using a selenomethionine-substituted enzyme. This recombinant PhTDH is a homo-tetramer in solution. Three monomers of PhTDHs were located in the crystallographic asymmetric unit, however, the crystal structure exhibits a homo-tetramer structure with crystallographic and non-crystallographic 222 symmetry in the cell. Despite the low level of sequence identity to a medium-chain NAD(H)-dependent alcohol dehydrogenase (ADH) and the different substrate specificity, the overall folds of the PhTDH monomer and tetramer are similar to those of the other ADH. Each subunit is composed of two domains: a nicotinamide cofactor (NAD(H))-binding domain and a catalytic domain. The NAD(H)-binding domain contains the alpha/beta Rossmann fold motif, characteristic of the NAD(H)-binding protein. One molecule of PhTDH contains one zinc ion playing a structural role. This metal ion exhibits coordination with four cysteine ligands and some of the ligands are conserved throughout the structural zinc-containing ADHs and TDHs. However, the catalytic zinc ion that is coordinated at the bottom of the cleft in the case of ADH was not observed in the crystal of PhTDH. There is a significant difference in the orientation of the catalytic domain relative to the coenzyme-binding domain that results in a larger interdomain cleft.
About this Structure
2DFV is a Single protein structure of sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA.
Reference
The first crystal structure of L-threonine dehydrogenase., Ishikawa K, Higashi N, Nakamura T, Matsuura T, Nakagawa A, J Mol Biol. 2007 Feb 23;366(3):857-67. Epub 2006 Nov 21. PMID:17188300
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