1qj5: Difference between revisions
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[[Image:1qj5.jpg|left|200px]] | [[Image:1qj5.jpg|left|200px]] | ||
'''CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE''' | {{Structure | ||
|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> | |||
|LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene> and <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] | |||
|GENE= BIOA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |||
}} | |||
'''CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1QJ5 is a [ | 1QJ5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QJ5 OCA]. | ||
==Reference== | ==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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10452893 10452893] | ||
[[Category: Adenosylmethionine--8-amino-7-oxononanoate transaminase]] | [[Category: Adenosylmethionine--8-amino-7-oxononanoate transaminase]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
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[[Category: pyridoxal-5'-phosphate]] | [[Category: pyridoxal-5'-phosphate]] | ||
''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 13:38:16 2008'' | ||
Revision as of 11:38, 20 March 2008
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| 1qj5, resolution 1.8Å | |||||||||||||
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| Sites: | LL1 and LL2 | ||||||||||||
| Ligands: | K and PLP | ||||||||||||
| Gene: | BIOA (Escherichia coli) | ||||||||||||
| Activity: | Adenosylmethionine--8-amino-7-oxononanoate transaminase, with EC number 2.6.1.62 | ||||||||||||
| 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
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