Superoxide DismutaseEC 1.15.1.1

Name (Group 13) Matric ID Section

Auni Aqilah binti Ahmad Tarmizi A13MB0212 02

Eka Latiffah Nadia binti Dzulkarnain A13MB0197 02

Nurul Nadiah binti Mohd Shuisma A13MB0198 01

Nurul Nasuha binti Muhamed Mukhtar A13MB0138 02

SMBB 3723 – BIOCOMPUTATION AND BIOINFORMATICS

ByDr. Mohd Shahir Shamsir bin Omar

Assignment 3

Introduction of Superoxide Dismutase (SOD)

Function Catalyzing the dismutation (or partioning) of the superoxide (O2−) radical into either ordinary molecular oxygen (O2) or hydrogen peroxide (H2O2). Type of enzyme that repairs cells and reduces the damage done to them by superoxide (the most common free radical). 4 types of of SOD enzymes:

Copper, Zinc SOD (Cu, Zn SOD) Manganese SOD (Mn SOD) – share same structural homology with Fe SOD Iron SOD (Fe SOD) Nickel SOD (Ni SOD)

Reaction:

History 1968: the enzymatic activity of SOD was discovered by – Irwin Fridovich and Joe McCord of Duke University.

Dr. Irwin Fridovich

Iron Superoxide Dismutase (FeSOD)

Prokaryotic enzyme. Found in chloroplast of plant, human mitochondria and some bacterial cells. The most primitive due to its presence in anaerobic bacteria and other prokaryotes. FeSODs are dimers with each iron active site containing a single iron bonded to three histidines, one aspartate and one water.

Industrial Applications Widely used in production of:

Cosmetics (reduce free radical damage to the skin – prevent wrinkle formations, reduce appearance of scars, lighten skin pigmentation caused by UV rays, and heal wounds). Product example is Paula’s Choice Skincare Range. Agriculture (SOD overexpress in transgenic plants improve plant resistance and tolerance to oxidative stress in various degrees). Food industry (SOD protect lipid, antioxidants and other preservatives by strongly inhibiting the reactions connected with production of superoxide  O2

- ion). Pharmaceuticals (antifibrotic drug, anti-inflammatory agent “Orgotein”, SOD supplement “SODzyme with GliSODin and Wolfberry”, and SOD creams for burns).

Major requirement: high rate of thermostability for commercial SOD – thermal denaturation is a cause of enzyme inactivation.Future prospects: gene therapy (the insertion of genes into an individual's cells and tissues to treat disease, such as cancer, where deleterious mutant alleles are replaced with functional ones).

Cosmetic product Pharmaceutical

product

PSYCHROPHILES

Psychrophiles are organisms which capable of growing in cold environment with

temperature ranges from -10⁰C - 20 ⁰ C. This extremophiles are present at polar regions,

high altitude places, glaciers and deep ocean.

Cold-adapted enzymes has been an enzyme of interest as it offers many advantages such as energy saving, easily inhibited by heating

when needed as well as reducing unnecessary chemical reaction that

happened at high temperature.

FeSOD from Aliivibrio salmonicida

Aliivibrio salmonicida is a cold adapted fish-

pathogenic bacteria which cause

cold-water vibriosis in Atlantic Salmon.

FeSOD from Aliivibrio salmonicida (2W7W)

Psychrophilic enzyme posses many uniques properties: 

Synthesize Caps (Cold acclimation proteins)

• Maintain membrane fluidity. 

• Replace cold-denatured peptides.

• Act as cold specific protease eliminating denatured protein.

• Maintain cell growth and cycle under low temperature

Synthesize of Antifreeze protein (AFPs) 

• Inhibit ice crystallization. 

Cryoprotectants

• Protect biological tissues from freezing damage.

Synthesize of housekeeping genes that are not repressed under low

temperature.

ADAPTATION

MESOPHILE

Uses

Medium temperature• between 20

- 45 °C (68 -113 °F). • Sewage- Escherichia

Coli• in cheese, yogurt-

Lactobacillus acidophilus

Disadvantages• human pathogen • can cause

food contamination and degradation in• Bread• Grains• Dairies• Meats3.Industrial

enzymes.

Uses

1.Dairy product

2.Brewing process

SUPEROXIDE DISMUTASE IN ESCHERICHIA COLIEscherichia coli

• Gram-negative• rod-shaped bacteria • inhabitant of the lower

gastrointestinal tract of warm-blooded animals

• possesses two genes encoding superoxide dismutases. • sodA encode the manganese-

containing enzymes • sodB, encode iron-containing

enzymes

SODs -protect the cells from the oxidative damage of superoxide radicals

when E. coli is exposed to dissolve O2 shift, the superoxide stress regulator SoxRS is activated and causes the stimulation of the superoxide dismutase system. This enables the E. coli to protect itself from the poisoning effects of oxygen

STRUCTURE

•mesophilic enzymes - superoxide dismutase • able to adapt in moderate temperature -room

temperature. • optimum temperature 0f 37°C.

•rigid and stable in room temperature • salt bridges around the active site-keep the active

site region together by opposing disorder due to greater atomic mobility at moderate temperature.

• hydrogen bonds -rigidify its mesophilic protein .• Van der Waals packing -stabilize the transmembrane

domains of membrane proteins

ADAPTIBILITY

THERMOPHILESThermophiles are microorganisms that are able to grow at elevated temperatures (45-80˚C) and can be found at places that have high

temperatures such as thermal vents, hot springs, sewage and marine sediments.

Thermostable enzymes are high in demand as they possess great advantages to the industry which includes the increase in rate of

reaction for most processes, reduce the possibility of contamination (unwanted microbial growth), reduce viscosity, and efficient mixing

process.

Origin of Thermostable FeSOD

Thermostable FeSOD can be found in the thermophile,

Thermosynechococcus elongatus. It is an obligate

photoautotrophic organism. T.elongatus has long been used as a model organism for the study of

photosynthesis.

STRUCTURE (1MY6)

Adaptations to High Temperature• The presence of heat shock proteins which is involved the folding

and unfolding of other proteins and prevent unwanted aggregation of protein.

• More charged residues (e.g arg, lys) form ion bonds that holds protein molecules together by weak bonds.

• High number of hydrogen bonds.• More hydrophobic interactions which prevents hot water from

entering the protein causing it to denature.• Fewer and shorter loop content and amino acid substitutions

cause more weak bonds between the loops and the whole protein structure.

• High number of disulphide bonds help stabilize protein structure.

Multiple Sequence Alignment(MSA)

Multiple Sequence Alignment is the alignment of 3 or more sequences which can be DNA, RNA or protein.

In this case, the alignment was done using sequences from three organisms which are Aliivibrio salmonicida (2W7W), Escherichia coli (2NYB) and Thermosynechococcus elongatus (1MY6). All of these organisms have Iron Superoxide Dismutase, but the adaptation of the enzyme to different temperatures vary.

These sequences are expected to have evolutionary relationship (heritable traits changes over generations).

Multiple Sequence Alignment provide informations on sequence homology as well as phylogenetic analysis.

Figure above is the output of ESPript in which these sequences are extracted from Protein Data Bank (PDB), then aligned with Clustal Omega. These sequences are grouped into three based on their similarities (conserved sequences).

Strictly conserved residues are indicated by red background.

Well conserved residues within a group are indicated by red letters. Remainder residues are indicated in black.

Residues conserved between groups are boxed

SUPERIMPOSED IMAGE

• superimpose image of psychrophilic, mesophilic and thermophilic superoxide dismutase.

• the region are mostly fit except for a loop on the thermophile that extended out (refer to the red circle in the picture above).• thermophilic enzyme has longer loops than mesophile and

psychrophile which is thought to be a mechanism for reducing unfolded state entropy.

• the longer surface loop lengths in thermophilic enzyme may have evolved in order to maintain its structure.

ACTIVE SITE

Homologous Fe superoxide dismutase usually has the same

arrangement or orientation of its 3D structures in the alpha-helices and the type of amino acid side chains

present at its active site.

A single Fe ion is present within the active site for iron-

dependent superoxide dismutase in a trigonal bipyramidal geometry

and attached by a hydrogen bond to

three histidines, an Aspartic acid , and an OH-/H2O molecule.