PDBsum entry 1a4e

Oxidoreductase

PDB id

1a4e

Contents

			Protein chains

					488 a.a. *

			Ligands

					AZI ×2


					SO4 ×2


					HEM ×2


					AZI-HEM ×2

			Waters ×957

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of catalase-A from saccharomyces cerevisiae.

Authors

M.J.Maté, M.Zamocky, L.M.Nykyri, C.Herzog, P.M.Alzari, C.Betzel, F.Koller, I.Fita.

Ref.

J Mol Biol, 1999, 286, 135-149. [DOI no: 10.1006/jmbi.1998.2453]

PubMed id

9931255

Abstract

The structure of the peroxisomal catalase A from the budding yeast Saccharomyces cerevisiae, with 515 residues per subunit, has been determined and refined to 2.4 A resolution. The crystallographic agreement factors R and Rfree are 15.4% and 19.8%, respectively. A tetramer with accurate 222-molecular symmetry is located in the asymmetric unit of the crystal. The conformation of the central core of catalase A, about 300 residues, remains similar to the structure of catalases from distantly related organisms. In contrast, catalase A lacks a carboxy-terminal domain equivalent to that found in catalase from Penicillium vitalae, the only other fungal catalase structure available. Structural peculiarities related with the heme and NADP(H) binding pockets can be correlated with biochemical characteristics of the catalase A enzyme. The network of molecular cavities and channels, filled with solvent molecules, supports the existence of one major substrate entry and at least two possible alternative pathways to the heme active site. The structure of the variant protein Val111Ala, also determined by X-ray crystallography at 2.8 A resolution, shows a few, well-localized, differences with respect to the wild-type enzyme. These differences, that include the widening of the entry channel in its narrowest point, provide an explanation for both the increased peroxidatic activity and the reduced catalatic activity of this mutant.



	Figure 5. Figure 5. Stereo views of the heme group environment in SCC-A. (a) side heme view and (b) view perpendicular to the heme plane. Carbon, oxygen and nitrogen atoms are represented as open, shaded and filled spheres, respectively. Hydrogen bonds are indicated by broken lines. The heme group, the azide molecule found in the distal side, the essential catalytic residues (His70, Ser109, Asn143, Arg351 and Tyr355), and two water molecules which are hydrogen-bonded to the propionic groups are explicitly shown in (a). The deprotonated oxygen of Tyr355, that makes two ionic hydrogen bonds with Arg351, acts as the proximal ligand of the iron atom (coordination is also indicated with a discontinuous bond). Residues that define the heme distal pocket are explicitly shown in (b). Asn68 interacts with Asp62 from the R related subunit (indicated by the symbol * in the Figure) and with a solvent molecule which starts a chain of water molecules that reach the central cavity of the catalase molecules (see the text). Neither the main-chain oxygen atom of cis-Pro69 nor the side-chain oxygen atom of Asn143 form standard hydrogen bonds and might interact with the heme ring.		Figure 7. Figure 7. Stereo view of the final (2F[o] - F[c]) electron density map showing the network of bonds that bridge the two pairs of heme groups in an SCC-A molecule (see the text and [Gouet et al 1995]). Heme groups and residues Asn60, Arg61, Asp357, together with four water molecules and two sulphate ions are also shown inside the density. The four subunits participate in each one of these heme-heme connections. Density for the azide molecules, situated in the heme distal pockets and coordinated with the iron atoms, can also be seen in this drawing. Sulfate ions are located on the molecular 2-fold axis P. The quality of the electron density allows to define unambiguously the hand of the heme group from the disposition of methyl and vinyl groups. For clarity only density situated till about 2.5 Å from the atoms represented is shown.

PROCHECK

	Headers