Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans

Abstract

Deinococcus radiodurans is an aerobic organism with the ability to survive under conditions of high radiation doses or desiccation. As part of its protection system against oxidative stress, this bacterium encodes three monofunctional catalases. The DR1998 catalase belongs to clade 1, and is present at high levels under normal growth conditions. The crystals of DR1998 diffracted very weakly, and the merged diffraction data showed an R sym of 0.308. Its crystal structure was determined and refined to 2.6 Å. The four molecules present in the asymmetric unit form, by crystallographic symmetry, two homotetramers with 222 point‐group symmetry. The overall structure of DR1998 is similar to that of other monofunctional catalases, showing higher structural homology with the catalase structures of clade 1. Each monomer shows the typical catalase fold, and contains one heme b in the active site. The heme is coordinated by the proximal ligand Tyr369, and on the heme distal side the essential His81 and Asn159 are hydrogen‐bonded to a water molecule. A 25‐Å‐long channel is the main channel connecting the active site to the external surface. This channel starts with a hydrophobic region from the catalytic heme site, which is followed by a hydrophilic region that begins on Asp139 and expands up to the protein surface. Apart from this channel, an alternative channel, also near the heme active site, is presented and discussed. Database Coordinates and structure factors have been deposited in the Protein Data Bank in Europe under accession code http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4CAB

Identification of coding sequence and its use for functional and structural characterization of catalase from Phyllanthus emblica

“…Conserved residues of the catalase sequence involved in the H2O2 binding (V 2, H 3, V 44, D 56, N 76, F 81, F 82, F 89) were identified after carefully studying the alignment. The results were found to be consistent with the experimentally determined crystallographic structures of human erythrocyte catalase (1QQW) [ 6 ] and Deinococcus radiodurans catalase (4CAB) [ 9 ]. However, few substitutions such as of isoleucine (I) by alanine (A), of methionine (M) by phenylalanine (F), of valine (V) by isoleucine (I) and of glutamine (Q) by leucine (L) were also observed in the translated CDS of catalase.…”

“…Catalases have been purified and structurally characterized from various microbial [ 5 , 6 , 7 , 8 , 9 ] and animal sources [ 10 ]. However, limited understanding of catalases function from rice [ 11 ] and wheat [ 12 ] is known using structural and functional data.…”

Structural features and functional implications of proteins enabling the robustness of Deinococcus radiodurans

“…The crystal structure of drKatE1 revealed a symmetric homotetramer with heme molecules in the active site ( Fig. 1 I) [58] . The protomer containing an alternative heme channel is very similar to previously solved monofunctional catalases, which indicates that drKatE1 is a highly conserved catalase.…”

“…Oxidoreductases play a critical role in antioxidation in D. radiodurans . At present, the structures of KatE1 [58] , MnSOD [59] , TrxR [27] and FrnE [60] have been determined. drKatE1 is a clade 1 type of monofunctional catalase.…”

Novel molecular insights into the anti‐oxidative stress response and structure–function of a salt‐inducible cyanobacterial Mn‐catalase

“…The commonly found catalases in prokaryotes are the typical haem catalases and the bifunctional catalase‐peroxidases (KatGs), both of which contain haem (Borges, Frazão, Miranda, Carrondo, & Romão, ; Njuma et al, ). However, another class of catalases that lack haem, called as non‐haem catalase or pseudocatalase, is present exclusively in prokaryotes and archaea (Andrews, ; Zámocký, Gasselhuber, Furtmüller, & Obinger, ).…”