PDBsum entry 1mgv

Transferase

PDB id: 1mgv

Contents

Protein chains

428 a.a. *

Ligands

PLP ×2

IPA ×4

Metals

_NA ×2

Waters ×342

* Residue conservation analysis

PDB id:

1mgv

Name:

Transferase

Title:

Crystal structure of the r391a mutant of 7,8-diaminopelargonic acid synthase

Structure:

7,8-diamino-pelargonic acid aminotransferase. Chain: a, b. Synonym: adenosylmethionine-8-amino-7-oxononanoate aminotransferase, dapa aminotransferase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: bioa. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.203 R-free: 0.233

Authors:

A.C.Eliot,J.Sandmark,G.Schneider,J.F.Kirsch

Key ref:

A.C.Eliot et al. (2002). The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation. Biochemistry, 41, 12582-12589. PubMed id: 12379100 DOI: 10.1021/bi026339a

Date:

16-Aug-02 Release date: 27-Nov-02

Protein chains

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

Seq: 429 a.a.

Struc: 428 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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: 10.1021/bi026339a

Biochemistry 41:12582-12589 (2002)

PubMed id: 12379100

The dual-specific active site of 7,8-diaminopelargonic acid synthase and the effect of the R391A mutation.

A.C.Eliot, J.Sandmark, G.Schneider, J.F.Kirsch.

ABSTRACT

7,8-diaminopelargonic acid (DAPA) synthase (EC 2.6.1.62) is a pyridoxal phosphate (PLP)-dependent transaminase that catalyzes the transfer of the alpha-amino group from S-adenosyl-L-methionine (SAM) to 7-keto-8-aminopelargonic acid (KAPA) to form DAPA in the antepenultimate step in the biosynthesis of biotin. The wild-type enzyme has a steady-state kcat value of 0.013 s(-1), and the K(m) values for SAM and KAPA are 150 and <2 microM, respectively. The k(max) and apparent K(m) values for the half-reaction of the PLP form of the enzyme with SAM are 0.016 s(-1) and 300 microM, respectively, while those for the reaction with DAPA are 0.79 s(-1) and 1 microM. The R391A mutant enzyme exhibits near wild-type kinetic parameters in the reaction with SAM, while the apparent K(m) for DAPA is increased 180-fold. The 2.1 A crystal structure of the R391A mutant enzyme shows that the mutation does not significantly alter the structure. These results indicate that the conserved arginine residue is not required for binding the alpha-amino acid SAM, but it is important for recognition of DAPA.