4K2B

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

Summary for 4K2B

• Entry DOI: 10.2210/pdb4k2b/pdb
• Related: 4K2I 4K2M
• Descriptor: NTD biosynthesis operon protein NtdA (2 entities in total)
• Functional Keywords: sugar aminotransferase, aspertate aminotransferase fold, homo-dimer, additional n-terninal domain, transferase
• Biological source: Bacillus subtilis subsp. subtilis
• Total number of polymer chains: 2
• Total formula weight: 100865.27

Authors

Van Straaten, K.E.,Palmer, D.R.J.,Sanders, D.A.R. (deposition date: 2013-04-08, release date: 2013-10-16, Last modification date: 2024-03-13)

Primary citation

van Straaten, K.E.,Ko, J.B.,Jagdhane, R.,Anjum, S.,Palmer, D.R.,Sanders, D.A.
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, 2013

PubMed 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.

PubMed: 24097983
DOI: 10.1074/jbc.M113.500637

Experimental method

X-RAY DIFFRACTION (2.31 Å)