3W21

Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase in complex with alpha-KG from Burkholderia ambifaria AMMD

Summary for 3W21

• Entry DOI: 10.2210/pdb3w21/pdb
• Related: 3W20
• Descriptor: Putative uncharacterized protein, ZINC ION, 2-OXOGLUTARIC ACID, ... (4 entities in total)
• Functional Keywords: dsbh fold, dioxygenase, zn, alpha-kg binding, oxidoreductase
• Biological source: Burkholderia ambifaria
• Total number of polymer chains: 2
• Total formula weight: 62621.99

Authors

Qin, H.M.,Miyakawa, T.,Jia, M.Z.,Nakamura, A.,Ohtsuka, J.,Xue, Y.L.,Kawashima, T.,Kasahara, T.,Hibi, M.,Ogawa, J.,Tanokura, M. (deposition date: 2012-11-26, release date: 2013-07-17, Last modification date: 2024-10-16)

Primary citation

Qin, H.M.,Miyakawa, T.,Jia, M.Z.,Nakamura, A.,Ohtsuka, J.,Xue, Y.L.,Kawashima, T.,Kasahara, T.,Hibi, M.,Ogawa, J.,Tanokura, M.
Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD
Plos One, 8:e63996-e63996, 2013

PubMed Abstract: A novel dioxygenase from Burkholderia ambifaria AMMD (SadA) stereoselectively catalyzes the C3-hydroxylation of N-substituted branched-chain or aromatic L-amino acids, especially N-succinyl-L-leucine, coupled with the conversion of α-ketoglutarate to succinate and CO2. To elucidate the structural basis of the substrate specificity and stereoselective hydroxylation, we determined the crystal structures of the SadA.Zn(II) and SadA.Zn(II).α-KG complexes at 1.77 Å and 1.98 Å resolutions, respectively. SadA adopted a double-stranded β-helix fold at the core of the structure. In addition, an HXD/EXnH motif in the active site coordinated a Zn(II) as a substitute for Fe(II). The α-KG molecule also coordinated Zn(II) in a bidentate manner via its 1-carboxylate and 2-oxo groups. Based on the SadA.Zn(II).α-KG structure and mutation analyses, we constructed substrate-binding models with N-succinyl-L-leucine and N-succinyl-L-phenylalanine, which provided new insight into the substrate specificity. The results will be useful for the rational design of SadA variants aimed at the recognition of various N-succinyl L-amino acids.

PubMed: 23724013
DOI: 10.1371/journal.pone.0063996

Experimental method

X-RAY DIFFRACTION (1.98 Å)