PDBsum entry 2a5h

Isomerase

PDB id: 2a5h

Contents

Protein chains

409 a.a.

Ligands

SO4 ×4

SAM ×4

LYS-PLP ×4

SF4 ×4

Metals

_ZN ×4

Waters ×608

References listed in PDB file

Key reference

Title

The X-Ray crystal structure of lysine-2,3-Aminomutase from clostridium subterminale.

Authors

B.W.Lepore, F.J.Ruzicka, P.A.Frey, D.Ringe.

Ref.

Proc Natl Acad Sci U S A, 2005, 102, 13819-13824. [DOI no: 10.1073/pnas.0505726102]

PubMed id

16166264

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.

Figure 4.
Fig. 4. Ball-and-stick, wall-eyed stereodiagram figure of the active site. This wall-eyed stereodiagram emphasizes the stereochemical relationships of the three cofactors, one as lysyl-PLP external aldimine. The C5' carbon of SeSAM where radical initiation will occur is 3.8 Å from C3 of the lysyl side chain. The conserved Arg-134 denies rotation around the C1-C2 bond of lysyl moiety. Asp-293 interacts with both the -amino group of lysine and N1 of the purine ring of SeSAM, and Asp-330 is in hydrogen-bonded contact with the -amino group. SeSAM is ligated to the unique iron in the [4Fe-4S] cluster through the selenomethionyl -amino and carboxylate groups. See Fig. 8 for detailed interactions within the active site. Hydrogen atom positions are provided for reference based on theoretical constraints only and are not determined by the diffraction data.

Figure 5.
Fig. 5. Close-up of the interaction between N1 of PLP and a fixed water molecule. This water molecule is held precisely in place in all four subunits by three main-chain hydrogen bonds from residues in the loop (R[112]YPDR[116]). The nature of the hydrogen bonding partners would uniquely position this water such that a water proton is hydrogen bonded with N1 of the pyridine nitrogen, implying that the pyridoxal ring is unprotonated.