Open AccessCrystal structure of NAD‐dependent formate dehydrogenase
Author(s) -
LAMZIN Victor S.,
ALESHIN Alexander E.,
STROKOPYTOV Boris V.,
YUKHNEVICH Maria G.,
POPOV Vladimir O.,
HARUTYUNYAN Emil H.,
WILSON Keith S.
Publication year - 1992
Publication title -
european journal of biochemistry
Language(s) - English
Resource type - Journals
eISSN - 1432-1033
pISSN - 0014-2956
DOI - 10.1111/j.1432-1033.1992.tb16945.x
Subject(s) - nad+ kinase , formate dehydrogenase , crystallography , multiple isomorphous replacement , cofactor , stereochemistry , chemistry , protein quaternary structure , ternary complex , oxidoreductase , dimer , active site , crystal structure , dehydrogenase , molecular replacement , peptide sequence , protein subunit , enzyme , biochemistry , organic chemistry , gene
The ternary complex of NAD‐dependent formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 (enzyme‐NAD‐azide) has been crystallised in the space group P2 1 2 1 2 1 with cell dimensions a = 11.60 nm, b = 11.33 nm, c = 6.34 nm. There is 1 dimeric molecule/asymmetric unit. An electron density map was calculated using phases from multiple isomorphous replacement at 0.30 nm resolution. Four heavy atom derivatives were used. The map was improved by solvent flattening and molecular averaging. The atomic model, including 2 × 393 amino acid residues, was refined by the CORELS and PROLSQ packages using data between 1.0 nm and 0.30 nm excluding structure factors less than 1 σ. The current R factor is 27.1% and the root mean square deviation from ideal bond lengths is 4.2 pm. The FDH subunit is folded into a globular two‐domain (coenzyme and catalytic) structure and the active centre and NAD binding site are situated at the domain interface. The β sheet in the FDH coenzyme binding domain contains an additional β strand compared to other dehydrogenases. The difference in quaternary structure between FDH and the other dehydrogenases means that FDH constitutes a new subfamily of NAD‐dependent dehydrogenases: namely the P‐oriented dimer. The FDH nucleotide binding region of the structure is aligned with the three dimensional structures of four other dehydrogenases and the conserved residues are discussed. The amino acid residues which contribute to the active centre and which make contact with NAD have been identified.