PDBsum entry 1v2e

Transferase

PDB id: 1v2e

Contents

Protein chains

368 a.a. *

Ligands

PLP ×2

KMT ×2

Waters ×87

* Residue conservation analysis

PDB id:

1v2e

Name:

Transferase

Title:

Crystal structure of t.Th hb8 glutamine aminotransferase complex with a-keto-g-methylthiobutyrate

Structure:

Glutamine aminotransferase. Chain: a, b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Gene: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.60Å R-factor: 0.231 R-free: 0.286

Authors:

M.Goto,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

M.Goto et al. (2004). Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition. J Biol Chem, 279, 16518-16525. PubMed id: 14761974 DOI: 10.1074/jbc.M311575200

Date:

15-Oct-03 Release date: 06-Jul-04

Protein chains

Q75WK2  (Q75WK2_THETH) -  Aminotransferase from Thermus thermophilus

Seq: 381 a.a.

Struc: 368 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.15 - glutamine--pyruvate transaminase.
• Reaction: L-glutamine + pyruvate = 2-oxoglutaramate + L-alanine

L-glutamine + pyruvate (Bound ligand (Het Group name = KMT) matches with 66.67% similarity) = 2-oxoglutaramate + L-alanine

• 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

reference

DOI no: 10.1074/jbc.M311575200

J Biol Chem 279:16518-16525 (2004)

PubMed id: 14761974

Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition.

M.Goto, R.Omi, I.Miyahara, A.Hosono, H.Mizuguchi, H.Hayashi, H.Kagamiyama, K.Hirotsu.

ABSTRACT

The following three-dimensional structures of three forms of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8 have been determined and represent the first x-ray analysis of the enzyme: the unliganded pyridoxal 5'-phosphate form at 1.9 A resolution and two complexes with 3-phenylpropionate and alpha-keto-gamma-methylthiobutyrate at 2.35 and 2.6 A resolution, respectively. The enzyme shows high activity toward phenylalanine, tyrosine, tryptophan, kynurenine, methionine, and glutamine. The enzyme is a homodimer, and each subunit is divided into an N-terminal arm and small and large domains. Based on its folding, the enzyme belongs to fold type I, aminotransferase subclass Ib. The subclass I aminotransferases whose structures have so far been determined exhibit a large movement of the small domain region upon binding of a substrate. Similarly, the glutamine:phenylpyruvate aminotransferase undergoes a large movement in part of the small domain to close the active site. The active-site pocket has a shape and size suitable to enclose the side chain of an aromatic amino acid or that of methionine. The inner side of the pocket is mostly hydrophobic, but also has polar sites. The kynurenine complex generated by computer modeling fits the pocket of the enzyme and its hydrophilic groups interact with the polar sites of the pocket.

Selected figure(s)

Figure 5.
FIG. 5. Schematic diagram showing hydrogen bond and salt bridge interactions of the active-site residues. Putative interactions are shown by dotted lines if the acceptor and donor are less than 3.5 Å apart. Phe-112 and Val-193, which sandwich the pyridine ring of PLP, are omitted for clarity. A, the unliganded ttGlnAT in the closed form. B, the ttGlnAT complex with 3PP. The hydrogen bonds between Ser-13 and Asp-113 have been omitted for clarity.

Figure 6.
FIG. 6. Superimposition of the active site of the ttGlnAT·kynurenine complex model onto ttGlnAT·3PP. The residues that represent the ttGlnAT· kynurenine complex and ttGlnAT·3PP are shown in brown and deep blue, respectively. Kynurenine and 3PP are represented by thick lines in pale blue and brown. The oxygen and nitrogen atoms of kynurenine and 3PP are colored red and deep blue, respectively. The dotted lines (green) show the hydrogen bonding interactions of the amino and carbonyl groups of the 3-anthraniloyl moiety of kynurenine with Asp-113 and Tyr-57^*, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 16518-16525) copyright 2004.

Figures were selected by an automated process.