1RCQ
The 1.45 A crystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms
Summary for 1RCQ
| Entry DOI | 10.2210/pdb1rcq/pdb |
| Related | 1BDO 1EPV 1L6F 1SFT 2SFP |
| Descriptor | catabolic alanine racemase DadX, PYRIDOXAL-5'-PHOSPHATE, D-LYSINE, ... (4 entities in total) |
| Functional Keywords | alpha-beta barrel, beta-structure for c-terminal domain, internal/external aldimine forms, isomerase |
| Biological source | Pseudomonas aeruginosa |
| Total number of polymer chains | 1 |
| Total formula weight | 39556.27 |
| Authors | Le Magueres, P.,Im, H.,Dvorak, A.,Strych, U.,Benedik, M.,Krause, K.L. (deposition date: 2003-11-04, release date: 2004-06-01, Last modification date: 2011-07-13) |
| Primary citation | LeMagueres, P.,Im, H.,Dvorak, A.,Strych, U.,Benedik, M.,Krause, K.L. Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms. Biochemistry, 42:14752-14761, 2003 Cited by PubMed Abstract: The structure of the catabolic alanine racemase, DadX, from the pathogenic bacterium Pseudomonas aeruginosa, reported here at 1.45 A resolution, is a dimer in which each monomer is comprised of two domains, an eight-stranded alpha/beta barrel containing the PLP cofactor and a second domain primarily composed of beta-strands. The geometry of each domain is very similar to that of Bacillus stearothermophilus alanine racemase, but the rotation between domains differs by about 15 degrees. This change does not alter the structure of the active site in which almost all residues superimpose well with a low rms difference of 0.86 A. Unexpectedly, the active site of DadX contains a guest substrate that is located where acetate and propionate have been observed in the Bacillus structures. It is modeled as d-lysine and oriented such that its terminal NZ atom makes a covalent bond with C4' of PLP. Since the internal aldimine bond between the protein lysine, Lys33, and C4' of PLP is also unambiguously observed, there appears to be an equilibrium between both internally and externally reacted forms. The PLP cofactor adopts two partially occupied conformational states that resemble previously reported internal and external aldimine complexes. PubMed: 14674749DOI: 10.1021/bi030165v PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.45 Å) |
Structure validation
Download full validation report
