Primary Citation PubMed: 12196534
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Dynamic mechanism of proton transfer in mannitol 2-dehydrogenase from Pseudomonas fluorescens: mobile GLU292 controls proton relay through a water channel that connects the active site with bulk solvent.
(2012) J Biol Chem 287
PubMed: 22194597 | PubMedCentral: PMC3307286 | DOI: 10.1074/jbc.M111.289223
Initial coordinates were taken from the crystal structures (binary complex with NAD + , PDB code 1LJ8 ; ternary complex with mannitol and NAD(H), PDB code 1M2W ).
The program PROPKA version 3.1 ( 48 ) was used to obtain estimates for the acid ionization constants (p K a values) for each residue in PDB 1LJ8 and 1M2W .
Panels A and B show close ups from the enzyme-NAD + (PDB 1LJ8 ) and the enzyme-NAD + -mannitol (PDB 1M2W ) crystal structures, respectively.
Structural dynamics of the enzyme as a whole is therefore explained from the overall trend of the simulation data to result from an opening movement of the C-terminal relative to the N-terminal domain, in useful agreement with the crystallographically observed reorientation of the two protein domains in 1M2W as compared with 1LJ8 (see supplemental Movie S2 ).
The mobility of Glu 292 is probably best represented in a superimposition of the trajectories for Glu 292 in protonated and unprotonated 1LJ8-NADH-fructose complexes ( Fig. 2 and supplemental Fig.
Modeling of fructose into 1LJ8 used the coordinates for mannitol from 1M2W, except that the C2 oxygen, which was modeled using Chimera ( 53 ), had a shorter bond length and slightly different dihedral angles.
Considering that the protein conformational change connected to formation of 1M2W from 1LJ8 could affect the ionization of different groups in and around the active site, particularly that of Glu 292 , we applied p K a calculations with PROPKA 3.1.
Publication Year: 2012
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
(2004) BMC Bioinformatics 5
PubMed: 15598351 | PubMedCentral: PMC544345 | DOI: 10.1186/1471-2105-5-197
One such example of a difficult but correctly assigned domain is the N-terminal domain of mannitol 2-dehydrogenase from Pseudomonas fluorescens (PDB code: 1lj8 [ 19 ], N-terminal domain; SCOP domain: ... 1lj8a2).
a) Ribbon diagram of mannitol 2-dehydrogenase from Pseudomonas fluorescens (PDB: 1lj8 ).
Publication Year: 2004
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