1td2
From Proteopedia
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|PDB= 1td2 |SIZE=350|CAPTION= <scene name='initialview01'>1td2</scene>, resolution 2.22Å | |PDB= 1td2 |SIZE=350|CAPTION= <scene name='initialview01'>1td2</scene>, resolution 2.22Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=PXL:3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE'>PXL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyridoxal_kinase Pyridoxal kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.35 2.7.1.35] </span> |
|GENE= PDXY, B1636 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= PDXY, B1636 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1td2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1td2 OCA], [http://www.ebi.ac.uk/pdbsum/1td2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1td2 RCSB]</span> | ||
}} | }} | ||
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[[Category: Scarsdale, N.]] | [[Category: Scarsdale, N.]] | ||
[[Category: Schirch, V.]] | [[Category: Schirch, V.]] | ||
| - | [[Category: PXL]] | ||
| - | [[Category: SO4]] | ||
[[Category: kinase]] | [[Category: kinase]] | ||
[[Category: pdxy]] | [[Category: pdxy]] | ||
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[[Category: ribokinase family]] | [[Category: ribokinase family]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:54:29 2008'' |
Revision as of 20:54, 30 March 2008
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| , resolution 2.22Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | PDXY, B1636 (Escherichia coli) | ||||||
| Activity: | Pyridoxal kinase, with EC number 2.7.1.35 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of the PdxY Protein from Escherichia coli
Overview
The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.
About this Structure
1TD2 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Crystal structure of the PdxY Protein from Escherichia coli., Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V, J Bacteriol. 2004 Dec;186(23):8074-82. PMID:15547280
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