Lydia Harvengt Jasmine Meyer

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Crystal  Structure  of  a  Manganese  Superoxide  Dismutase:  Deninoccus  radiodurans  

(a)  Function  Superoxide  dismutase  is  one  of  the  most  important  enzymes  in  the  world.    It  comes  in  

several  forms  in  different  organisms,  but  all  have  the  same  function:  to  nullify  superoxides.    All  

superoxides  contain  a  highly  reactive  form  of  oxygen  containing  an  unpaired  electron,  and  have  

the  formula  O2-­‐.    Superoxides  are  toxic,  and  can  cause  DNA  mutation  and  other  problems  within  

cells,  and  are  often  created  by  misdirected  electron  transfer  in  respiratory  enzymes.1    A  general  

superoxide  dismutase  reaction  will  remove  the  lone  electron  from  one  superoxide  species  to  

make  normal  oxygen  and  transfer  it  to  another  superoxide  species,  which  will  be  converted  to  

hydrogen  peroxide.1    This  overview  is  looking  specifically  at  the  function  of  a  manganese  

superoxide  dismutase,  which  is  only  found  in  mitochondria.2    This  particular  manganese  

superoxide  comes  from  Deinococcus  radiodurans  (DEIRA),  which  are  “the  world’s  toughest  

bacterium”  according  to  the  Guinness  Book  of  World  Records.3    They  can  survive  drought,  acidic  

conditions,  cold  temperatures,  and  extreme  nutrient  deficiency.    In  addition,  they  are  the  most  

radiation-­‐resistant  organisms  known.4    Two  crystal  structures  were  determined  for  DR1279,  

shown  in  Figure  1,  but  the  focus  will  be  on  the  first  of  these  two  (Figure  1).4  

 

Figure  1:  The  two  crystal  structures  illucidated  for  the  superoxide  dismutase  protein  

 

 

 

 

   

 (1) Goodsell, D. Protein Data Bank. http://www.rcsb.org/pdb/101/motm.do?momID=94 (accessed March 14, 2014). (2)  Borgstahl, B. E.; Pokross, M.; Chehab, R.; Sekher, A; Snell, E. H. J. Mol. Biol. 2000, 296, 951-959. (3)  Venkateswaran, A.; McFarlan, S. C.; Ghosal, D.; Minton, K. W.; Vasilenko, A.; Makarova, K.; Wackett, L. P.; Daly, M. J. Appl Environ Microbiol. 2000, 66, 2620-2626. (4)  Dennis, R. J.; Micossi, E.; McCarthy, J.; Moe, E.; Gordan, E. J.; Kozielski-Stuhrmann, S.; Leonard, G. A.; McSweeney, S. Acta Crystallogr. Sect F Struct. Biol. Cryst. Commun. 2006, 62, 325-329.    

Lydia Harvengt Jasmine Meyer

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(b) Structural Analysis of DEIRA

The structure of a manganese superoxide dismutase found in Deninoccus radioduransis

(DEIRA) is diagramed in three images in Figure 2. As noted previously, DEIRA has strong

radiation resistant properties, and these properties have been experimentally linked to the

presence of an Mn-SOD protein.4 This protein is labelled 2CE4 in the protein database and

belongs to the space group P21.4 DEIRA has a characteristic trigonal bipyramidal shape. Its

dimensional structure and mechanism of action is similar to that of a manganese superoxide

dismutase isolated from E. coli, which also has a similar amino acid sequence.4 The manganese

is a penta-coordinate metal, that is, five ligands are attached to it. The five ligands are OH at

position 1, three histidines at positions 26, 81, and 171, and an aspartic acid at position 167

(Figure 2). There were several characteristic bond lengths and angles. The bond length between

the manganese and a nitrogen atom was 11.5 Å. The bond length between the manganese and

oxygen is 1.5 Å. The angle between these two bonds is 45.4º. The structure of DIERA is

essential to its characteristic properties, such as its strong resistance to ionizing radiation.

Figure 2: The image on the left shows manganese in the center of the image in lavender and was produced with Jmol. The center image shows only the amino acids which are coordinated to the manganese (5).5 The image on the far right shows the penta-coordinate structure.2

 (5) Oswasa, M.; Yamakura, F.; Mihara, M.; Okubo, Y.; Hiraoka, Y. B. Biochim. Biophys. Acta 2010, 1804, 1775-1779.

 

Lydia Harvengt Jasmine Meyer

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(c) Mechanism of Catalysis

The proposed mechanism of the manganese superoxide dismutase is shown in Scheme 1.

The manganese begins in a penta-coordinate system with oxidation state +3. A superoxide (O2-)

molecule then coordinates to the manganese, resulting in a hexa-coordinate system around the

manganese. Then the hydroxide ligand becomes protonated, creating a water ligand, and

allowing an electron to be transferred from the superoxide ligand to the metal, which leaves as

neutral oxygen (O2). The manganese is now in the lower oxidation state +2. A second

superoxide molecule then attacks the manganese, moving the active site back into a hexa-

coordinate geometry. This second time, the electron transfer goes in the opposite direction, from

the metal to the O2 ligand, and results in the formation of Mn3+ and O22-. The O2

2- is being

protonated as it is formed. One proton comes from the water ligand, which again becomes a

hydroxide, and the addition of a second and final proton generates hydrogen peroxide (H2O2).

The net result of this mechanism is the disproportionation of two superoxide molecules into an

oxygen molecule and a hydrogen peroxide molecule, as is characteristic of superoxide

dismutases in general.

Lydia Harvengt Jasmine Meyer

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Scheme 1: The four-step mechanism of action of the manganese superoxide dismutase.6

 (6) Holm, R. H.; Kennepohl, P.; Solomon, E. I. Chem. Rev. 1996, 96, 2239-2314.

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(d) Molecular Model

In order for the manganese active site to transform dangerous superoxide molecules,

there must be a pocket through which the superoxide can enter and bind in the coordination

sphere. This site and pocket can be seen in Figure 3. Representations of both the high and low

oxidation states of manganese are shown Figure 3, and the main difference consists in the

presence or absence of an additional charge on the hydroxyl group. As was seen in the

mechanism in Scheme 1, manganese in both oxidation states must be prepared to accept an

additional superoxide ligand. Therefore, both sets of images show a clear pocket, which in the

upper set of images is shown full on, and in the second set of images is shown at an angle. The

specific angles and bond lengths in this region were discussed during the structural analysis.

Figure 3: Models of the active site in the absense of oxygen. The top row represents the high oxidation state (+3) and the bottom row represents the low oxidation state. From left to right, the representations are shown as ball and stick, stick, and space filling models.