1qj5
From Proteopedia
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==Overview== | ==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 ... | + | 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== | ==About this Structure== | ||
| - | 1QJ5 is a | + | 1QJ5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with K and PLP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Structure known Active Sites: LL1 and LL2. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QJ5 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: pyridoxal-5'-phosphate]] | [[Category: pyridoxal-5'-phosphate]] | ||
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 14:03:12 2007'' |
Revision as of 11:57, 5 November 2007
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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 with K and PLP as ligands. Active as Adenosylmethionine--8-amino-7-oxononanoate transaminase, with EC number 2.6.1.62 Structure known Active Sites: LL1 and LL2. 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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