PDBsum entry 4k2b

Transferase

PDB id: 4k2b

Contents

Protein chains

437 a.a.

Waters ×516

PDB id:

4k2b

Name:

Transferase

Title:

Crystal structure of ntda from bacillus subtilis in complex with the internal aldimine

Structure:

Ntd biosynthesis operon protein ntda. Chain: a, b. Engineered: yes

Source:

Bacillus subtilis subsp. Subtilis. Organism_taxid: 224308. Strain: 168. Gene: 939788, bsu10550, np_388936.1, ntda, yhjl. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.31Å R-factor: 0.163 R-free: 0.214

Authors:

K.E.Van Straaten,D.R.J.Palmer,D.A.R.Sanders

Key ref:

K.E.van Straaten et al. (2013). The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new subclass of aminotransferases. J Biol Chem, 288, 34121-34130. PubMed id: 24097983 DOI: 10.1074/jbc.M113.500637

Date:

08-Apr-13 Release date: 16-Oct-13

Protein chains

O07566  (NTDA_BACSU) -  3-oxo-glucose-6-phosphate:glutamate aminotransferase from Bacillus subtilis (strain 168)

Seq: 441 a.a.

Struc: 437 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.6.1.104 - 3-dehydro-glucose-6-phosphate--glutamate transaminase.
• Reaction: 3-dehydro-D-glucose 6-phosphate + L-glutamate = D-kanosamine 6-phosphate + 2-oxoglutarate
• Cofactor: Pyridoxal 5'-phosphate

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

reference

DOI no: 10.1074/jbc.M113.500637

J Biol Chem 288:34121-34130 (2013)

PubMed id: 24097983

The structure of NtdA, a sugar aminotransferase involved in the kanosamine biosynthetic pathway in Bacillus subtilis, reveals a new subclass of aminotransferases.

K.E.van Straaten, J.B.Ko, R.Jagdhane, S.Anjum, D.R.Palmer, D.A.Sanders.

ABSTRACT

NtdA from Bacillus subtilis is a sugar aminotransferase that catalyzes the pyridoxal phosphate-dependent equatorial transamination of 3-oxo-α-d-glucose 6-phosphate to form α-d-kanosamine 6-phosphate. The crystal structure of NtdA shows that NtdA shares the common aspartate aminotransferase fold (Type 1) with residues from both monomers forming the active site. The crystal structures of NtdA alone, co-crystallized with the product α-d-kanosamine 6-phosphate, and incubated with the amine donor glutamate reveal three key structures in the mechanistic pathway of NtdA. The structure of NtdA alone reveals the internal aldimine form of NtdA with the cofactor pyridoxal phosphate covalently attached to Lys-247. The addition of glutamate results in formation of pyridoxamine phosphate. Co-crystallization with kanosamine 6-phosphate results in the formation of the external aldimine. Only α-d-kanosamine 6-phosphate is observed in the active site of NtdA, not the β-anomer. A comparison of the structure and sequence of NtdA with other sugar aminotransferases enables us to propose that the VIβ family of aminotransferases should be divided into subfamilies based on the catalytic lysine motif.