1qj5
From Proteopedia
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|PDB= 1qj5 |SIZE=350|CAPTION= <scene name='initialview01'>1qj5</scene>, resolution 1.8Å | |PDB= 1qj5 |SIZE=350|CAPTION= <scene name='initialview01'>1qj5</scene>, resolution 1.8Å | ||
|SITE= <scene name='pdbsite=LL1:Pyridoxal-5'-Phosphate+Binding+Site'>LL1</scene> and <scene name='pdbsite=LL2:Pyridoxal-5'-Phosphate+Binding+Site'>LL2</scene> | |SITE= <scene name='pdbsite=LL1:Pyridoxal-5'-Phosphate+Binding+Site'>LL1</scene> and <scene name='pdbsite=LL2:Pyridoxal-5'-Phosphate+Binding+Site'>LL2</scene> | ||
| - | |LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene> | + | |LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5'-PHOSPHATE'>PLP</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Adenosylmethionine--8-amino-7-oxononanoate_transaminase Adenosylmethionine--8-amino-7-oxononanoate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.62 2.6.1.62] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosylmethionine--8-amino-7-oxononanoate_transaminase Adenosylmethionine--8-amino-7-oxononanoate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.62 2.6.1.62] </span> |
|GENE= BIOA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= BIOA ([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=1qj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qj5 OCA], [http://www.ebi.ac.uk/pdbsum/1qj5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qj5 RCSB]</span> | ||
}} | }} | ||
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[[Category: Sandmark, J.]] | [[Category: Sandmark, J.]] | ||
[[Category: Schneider, G.]] | [[Category: Schneider, G.]] | ||
| - | [[Category: K]] | ||
| - | [[Category: PLP]] | ||
[[Category: aminotransferase]] | [[Category: aminotransferase]] | ||
[[Category: biotin biosynthesis]] | [[Category: biotin biosynthesis]] | ||
[[Category: pyridoxal-5'-phosphate]] | [[Category: pyridoxal-5'-phosphate]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:14:31 2008'' |
Revision as of 20:14, 30 March 2008
| |||||||
| , resolution 1.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | and | ||||||
| Ligands: | , | ||||||
| Gene: | BIOA (Escherichia coli) | ||||||
| Activity: | Adenosylmethionine--8-amino-7-oxononanoate transaminase, with EC number 2.6.1.62 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE
Overview
The three-dimensional structure of diaminopelargonic acid synthase, a vitamin B6-dependent enzyme in the pathway of the biosynthesis of biotin, has been determined to 1.8 A resolution by X-ray crystallography. The structure was solved by multi-wavelength anomalous diffraction techniques using a crystal derivatized with mercury ions. The protein model has been refined to a crystallographic R -value of 17.5% (R -free 22.6%). Each enzyme subunit consists of two domains, a large domain (residues 50-329) containing a seven-stranded predominantly parallel beta-sheet, surrounded by alpha-helices, and a small domain comprising residues 1-49 and 330-429. Two subunits, related by a non-crystallographic dyad in the crystals, form the homodimeric molecule, which contains two equal active sites. Pyridoxal-5'-phosphate is bound in a cleft formed by both domains of one subunit and the large domain of the second subunit. The cofactor is anchored to the enzyme by a covalent linkage to the side-chain of the invariant residue Lys274. The phosphate group interacts with main-chain nitrogen atoms and the side-chain of Ser113, located at the N terminus of an alpha-helix. The pyridine nitrogen forms a hydrogen bond to the side-chain of the invariant residue Asp245. Electron density corresponding to a metal ion, most likely Na(+), was found in a tight turn at the surface of the enzyme. Structure analysis reveals that diaminopelargonic acid synthase belongs to the family of vitamin B6-dependent aminotransferases with the same fold as originally observed in aspartate aminotransferase. A multiple structure alignment of enzymes in this family indicated that they form at least six different subclasses. Striking differences in the fold of the N-terminal part of the polypeptide chain are one of the hallmarks of these subclasses. Diaminopelargonic acid synthase is a member of the aminotransferase subclass III. From the structure of the non-productive complex of the holoenzyme with the substrate 7-keto-8-aminopelargonic acid the location of the active site and residues involved in substrate binding have been identified.
About this Structure
1QJ5 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes., Kack H, Sandmark J, Gibson K, Schneider G, Lindqvist Y, J Mol Biol. 1999 Aug 27;291(4):857-76. PMID:10452893
Page seeded by OCA on Sun Mar 30 23:14:31 2008
