PDBsum entry 1qj3

Transferase

PDB id: 1qj3

Contents

Protein chains

416 a.a. *

Ligands

PLP ×2

KAP ×2

Metals

_NA ×2

Waters ×94

* Residue conservation analysis

PDB id:

1qj3

Name:

Transferase

Title:

Crystal structure of 7,8-diaminopelargonic acid synthase in complex with 7-keto-8-aminopelargonic acid

Structure:

7,8-diaminopelargonic acid synthase. Chain: a, b. Engineered: yes

Source:

Escherichia coli bl21(de3). Organism_taxid: 469008. Cellular_location: cytoplasm. Gene: bioa. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.70Å R-factor: 0.225 R-free: 0.279

Authors:

H.Kaeck,J.Sandmark,K.J.Gibson,Y.Lindqvist,G.Schneider

Key ref:

H.Käck et al. (1999). Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes. J Mol Biol, 291, 857-876. PubMed id: 10452893 DOI: 10.1006/jmbi.1999.2997

Date:

21-Jun-99 Release date: 22-Jun-00

Protein chains

P12995  (BIOA_ECOLI) -  Adenosylmethionine-8-amino-7-oxononanoate aminotransferase from Escherichia coli (strain K12)

Seq: 429 a.a.

Struc: 416 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.6.1.62 - adenosylmethionine--8-amino-7-oxononanoate transaminase.
• Reaction: (8S)-8-amino-7-oxononanoate + S-adenosyl-L-methionine = S-adenosyl-4- methylsulfanyl-2-oxobutanoate + (7R,8S)-7,8-diammoniononanoate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1006/jmbi.1999.2997

J Mol Biol 291:857-876 (1999)

PubMed id: 10452893

Crystal structure of diaminopelargonic acid synthase: evolutionary relationships between pyridoxal-5'-phosphate-dependent enzymes.

H.Käck, J.Sandmark, K.Gibson, G.Schneider, Y.Lindqvist.

ABSTRACT

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.

Selected figure(s)

Figure 1.
Figure 1. The reaction catalysed by DAPA synthase follows a ping-pong mechanism and goes through two half-reactions for each complete cycle of transamination. SAM is the first substrate and binds to the PLP form of DAPA synthase. After the first reaction step, the amino group of SAM has been transferred to the cofactor, which as a result is converted into its pyridoxamine form, and the first product leaves the active site. In the second half-reaction, the second substrate, KAPA, binds to the active site, receives an amino group from pyri- doxamine phosphate and is thus converted to DAPA. In this process PLP is regenerated.

Figure 2.
Figure 2. Reaction scheme for the first half of an aminotransferase reaction.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 291, 857-876) copyright 1999.

Figures were selected by an automated process.