1wyu
From Proteopedia
(New page: 200px<br /><applet load="1wyu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wyu, resolution 2.10Å" /> '''Crystal structure of...) |
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| - | [[Image:1wyu.gif|left|200px]]<br /><applet load="1wyu" size=" | + | [[Image:1wyu.gif|left|200px]]<br /><applet load="1wyu" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wyu, resolution 2.10Å" /> | caption="1wyu, resolution 2.10Å" /> | ||
'''Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form'''<br /> | '''Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the P-protein of the glycine cleavage system from | + | The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia. |
==About this Structure== | ==About this Structure== | ||
| - | 1WYU is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with PLP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] Full crystallographic information is available from [http:// | + | 1WYU is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYU OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Nakagawa, N.]] | [[Category: Nakagawa, N.]] | ||
[[Category: Nakai, T.]] | [[Category: Nakai, T.]] | ||
| - | [[Category: RSGI, RIKEN | + | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] |
[[Category: PLP]] | [[Category: PLP]] | ||
[[Category: alpha(2)beta(2) tetramer]] | [[Category: alpha(2)beta(2) tetramer]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:49:27 2008'' |
Revision as of 13:49, 21 February 2008
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Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in holo form
Overview
The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.
About this Structure
1WYU is a Protein complex structure of sequences from Thermus thermophilus with as ligand. Active as Glycine dehydrogenase (decarboxylating), with EC number 1.4.4.2 Full crystallographic information is available from OCA.
Reference
Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia., Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N, EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:15791207
Page seeded by OCA on Thu Feb 21 15:49:27 2008
Categories: Glycine dehydrogenase (decarboxylating) | Protein complex | Thermus thermophilus | Kamiya, N. | Kuramitsu, S. | Maoka, N. | Masui, R. | Nakagawa, N. | Nakai, T. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | PLP | Alpha(2)beta(2) tetramer | Riken structural genomics/proteomics initiative | Rsgi | Structural genomics
