PDBsum entry 1c9c

Transferase

PDB id: 1c9c

Contents

Protein chain

396 a.a. *

Ligands

PP3

Waters ×117

* Residue conservation analysis

PDB id:

1c9c

Name:

Transferase

Title:

Aspartate aminotransferase complexed with c3-pyridoxal-5'-phosphate

Structure:

Aspartate aminotransferase. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.40Å R-factor: 0.202 R-free: 0.269

Authors:

J.Ishijima,T.Nakai,S.Kawaguchi,K.Hirotsu,S.Kuramitsu

Key ref:

J.Ishijima et al. (2000). Free energy requirement for domain movement of an enzyme. J Biol Chem, 275, 18939-18945. PubMed id: 10858450 DOI: 10.1074/jbc.275.25.18939

Date:

02-Aug-99 Release date: 20-Dec-00

Protein chain

P00509  (AAT_ECOLI) -  Aspartate aminotransferase from Escherichia coli (strain K12)

Seq: 396 a.a.

Struc: 396 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.1 - aspartate transaminase.
• Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PP3) matches with 68.18% similarity)

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

reference

DOI no: 10.1074/jbc.275.25.18939

J Biol Chem 275:18939-18945 (2000)

PubMed id: 10858450

Free energy requirement for domain movement of an enzyme.

J.Ishijima, T.Nakai, S.Kawaguchi, K.Hirotsu, S.Kuramitsu.

ABSTRACT

Domain movement is sometimes essential for substrate recognition by an enzyme. X-ray crystallography of aminotransferase with a series of aliphatic substrates showed that the domain movement of aspartate aminotransferase was changed dramatically from an open to a closed form by the addition of only one CH(2) to the side chain of the C4 substrate CH(3)(CH(2))C((alpha))H(NH(3)(+))COO(-). These crystallographic results and reaction kinetics (Kawaguchi, S., Nobe, Y., Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem. (Tokyo) 122, 55-63; Kawaguchi, S. and Kuramitsu, S. (1998) J. Biol. Chem. 273, 18353-18364) enabled us to estimate the free energy required for the domain movement.

Selected figure(s)

Figure 2.
Fig. 2. The mechanisms of domain movement. The -helix 1 (Ile^17-Arg25) and the loop region (Ala^26-Ile^37) of the C3-PLP or C4-PLP complex in the open form (these residues are colored pink and the others gray) change to the closed form on binding of C5-PLP or C6-PLP (colored green). Ile^17 and Ile^37 are anchored at the active site by hydrophobic interactions with the substrate. Leu18 is located at the N-terminal end of -helix 1 and pulls the helix into the active pocket to shield the active site from the solvent. This tugging of residues from Ile^17 to Ile^37 changes the enzyme from the open to the closed form.

Figure 3.
Fig. 3. Stereoviews of AspAT bound to substrate analogs. Only Arg292* and the substrate analogs are indicated for clarity. a, the substrate analog is C4-PLP (the moiety of coenzyme is labeled as PLP and that of substrate as C4). The active-site conformation of the C4-PLP complex is almost identical to that of substrate-free AspAT (8, 9). b, the substrate analog is C5-PLP. Each substrate analog and the side chain of Arg292* are superimposed onto the (F[o] F[c]) omit map contoured at 2.5 (a) and 3 (b) with these atoms omitted. c, the structure of the C3-PLP complex (magenta), C4-PLP complex (yellow), C5-PLP complex (cyan), and C6-PLP complex (green). Note that the side chain orientation of Arg292* changes drastically depending on substrate. These figures were produced using the program O (23).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 18939-18945) copyright 2000.

Figures were selected by an automated process.