2A5H

2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).

Summary for 2A5H

• Entry DOI: 10.2210/pdb2a5h/pdb
• Descriptor: L-lysine 2,3-aminomutase, ZINC ION, SULFATE ION, ... (8 entities in total)
• Functional Keywords: radical sam, four-iron-four-sulfur cluster, 4fe4s, fs4, sam, s-adenosylmethionine, alpha-beta channel, pyridoxal-5'-phosphate, external aldimine, michaelis analog, isomerase
• Biological source: Clostridium subterminale
• Total number of polymer chains: 4
• Total formula weight: 195763.48

Authors

Lepore, B.W.,Ruzicka, F.J.,Frey, P.A.,Ringe, D. (deposition date: 2005-06-30, release date: 2005-10-04, Last modification date: 2025-03-26)

Primary citation

Lepore, B.W.,Ruzicka, F.J.,Frey, P.A.,Ringe, D.
The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale.
Proc.Natl.Acad.Sci.Usa, 102:13819-13824, 2005

PubMed Abstract: The x-ray crystal structure of the pyridoxal-5'-phosphate (PLP), S-adenosyl-L-methionine (SAM), and [4Fe-4S]-dependent lysine-2,3-aminomutase (LAM) of Clostridium subterminale has been solved to 2.1-A resolution by single-wavelength anomalous dispersion methods on a L-selenomethionine-substituted complex of LAM with [4Fe-4S]2+, PLP, SAM, and L-alpha-lysine, a very close analog of the active Michaelis complex. The unit cell contains a dimer of hydrogen-bonded, domain-swapped dimers, the subunits of which adopt a fold that contains all three cofactors in a central channel defined by six beta/alpha structural units. Zinc coordination links the domain-swapped dimers. In each subunit, the solvent face of the channel is occluded by an N-terminal helical domain, with the opposite end of the channel packed against the domain-swapped subunit. Hydrogen-bonded ionic contacts hold the external aldimine of PLP and L-alpha-lysine in position for abstraction of the 3-pro-R hydrogen of lysine by C5' of SAM. The structure of the SAM/[4Fe-4S] complex confirms and extends conclusions from spectroscopic studies of LAM and shows selenium in Se-adenosyl-L-selenomethionine poised to ligate the unique iron in the [4Fe-4S] cluster upon electron transfer and radical formation. The chain fold in the central domain is in part analogous to other radical-SAM enzymes.

PubMed: 16166264
DOI: 10.1073/pnas.0505726102

Experimental method

X-RAY DIFFRACTION (2.1 Å)