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PDBsum entry 1gn3

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1gn3
Jmol
Contents
Protein chains
198 a.a. *
Metals
_FE ×2
* Residue conservation analysis
PDB id:
1gn3
Name: Oxidoreductase
Title: H145q mutant of mycobacterium tuberculosis iron-superoxide dismutase.
Structure: Superoxide dismutase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: mycobacterium vaccae. Expression_system_taxid: 1810
Biol. unit: Tetramer (from PDB file)
Resolution:
4.00Å     R-factor:   0.168     R-free:   0.184
Authors: K.A.Bunting,J.B.Cooper,M.O.Badasso,I.J.Tickle,M.Newton, S.P.Wood,Y.Zhang,D.B.Young
Key ref:
K.Bunting et al. (1998). Engineering a change in metal-ion specificity of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis-- X-ray structure analysis of site-directed mutants. Eur J Biochem, 251, 795-803. PubMed id: 9490054 DOI: 10.1046/j.1432-1327.1998.2510795.x
Date:
02-Oct-01     Release date:   05-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WGE6  (SODF_MYCTO) -  Superoxide dismutase [Fe]
Seq:
Struc:
207 a.a.
198 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.15.1.1  - Superoxide dismutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 superoxide + 2 H+ = O2 + H2O2
2 × superoxide
+ 2 × H(+)
= O(2)
+ H(2)O(2)
      Cofactor: Fe cation or Mn(2+) or (Zn(2+) and Cu cation)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     protein binding     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1046/j.1432-1327.1998.2510795.x Eur J Biochem 251:795-803 (1998)
PubMed id: 9490054  
 
 
Engineering a change in metal-ion specificity of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis-- X-ray structure analysis of site-directed mutants.
K.Bunting, J.B.Cooper, M.O.Badasso, I.J.Tickle, M.Newton, S.P.Wood, Y.Zhang, D.Young.
 
  ABSTRACT  
 
We have refined the X-ray structures of two site-directed mutants of the iron-dependent superoxide dismutase (SOD) from Mycobacterium tuberculosis. These mutations which affect residue 145 in the enzyme (H145Q and H145E) were designed to alter its metal-ion specificity. This residue is either Gln or His in homologous SOD enzymes and has previously been shown to play a role in active-site interactions since its side-chain helps to coordinate the metal ion via a solvent molecule which is thought to be a hydroxide ion. The mutations were based on the observation that in the closely homologous manganese dependent SOD from Mycobacterium leprae, the only significant difference from the M. tuberculosis SOD within 10 A of the metal-binding site is the substitution of Gln for His at position 145. Hence an H145Q mutant of the M. tuberculosis (TB) SOD was engineered to investigate this residue's role in metal ion dependence and an isosteric H145E mutant was also expressed. The X-ray structures of the H145Q and H145E mutants have been solved at resolutions of 4.0 A and 2.5 A, respectively, confirming that neither mutation has any gross effects on the conformation of the enzyme or the structure of the active site. The residue substitutions are accommodated in the enzyme's three-dimensional structure by small local conformational changes. Peroxide inhibition experiments and atomic absorption spectroscopy establish surprisingly the H145E mutant SOD has manganese bound to it whereas the H145Q mutant SOD retains iron as the active-site metal. This alteration in metal specificity may reflect on the preference of manganese ions for anionic ligands.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. The electron density (2FO -FC ) contours for the active site in the H145Q mutant structure. The Gln145 side chain is on the right hand side. It has refined to a conformation in which it forms interactions similar to those found in other SOD structures possessing glutamine at this position. The low resolution of the data do not justify inclusion of the active site solvent molecule which is normally located between the metal ion and residue 145. The map is contoured at 1.0 rms.
Figure 5.
Fig. 5. The electron density (2F O -F C) contours for the active site residues in the H145E mutant structure. The resolution of the map is 2.5 A and contours at the 1.0 rms level are shown. Glu145 is on the right. SOLV indicates the putative hydroxide ion ligand.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (1998, 251, 795-803) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19191037 T.Wang, A.Qiu, F.Meng, and H.Zhou (2009).
Changing the Metal Binding Specificity of Superoxide Dismutase from Thermus thermophilus HB-27 by a Single Mutation.
  Mol Biotechnol, 42, 146-153.  
17912757 R.Wintjens, D.Gilis, and M.Rooman (2008).
Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence.
  Proteins, 70, 1564-1577.  
12897839 J.Maréchal, R.Santos, Y.Hammad, N.Alloisio, A.M.Domenach, and P.Normand (2003).
Characterization of the sodF gene region of Frankia sp. strain ACN14a and complementation of Escherichia coli sod mutant.
  Can J Microbiol, 49, 294-300.  
12730184 L.C.Tabares, C.Bittel, N.Carrillo, A.Bortolotti, and N.Cortez (2003).
The single superoxide dismutase of Rhodobacter capsulatus is a cambialistic, manganese-containing enzyme.
  J Bacteriol, 185, 3223-3227.  
12392545 T.Hunter, J.V.Bannister, and G.J.Hunter (2002).
Thermostability of manganese- and iron-superoxide dismutases from Escherichia coli is determined by the characteristic position of a glutamine residue.
  Eur J Biochem, 269, 5137-5148.  
11141052 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Outer sphere mutations perturb metal reactivity in manganese superoxide dismutase.
  Biochemistry, 40, 15-27.
PDB codes: 1en4 1en5 1en6
11294629 R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, and G.B.Jameson (2001).
Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity.
  Biochemistry, 40, 4622-4632.
PDB codes: 1i08 1i0h
9933629 G.Harth, and M.A.Horwitz (1999).
Export of recombinant Mycobacterium tuberculosis superoxide dismutase is dependent upon both information in the protein and mycobacterial export machinery. A model for studying export of leaderless proteins by pathogenic mycobacteria.
  J Biol Chem, 274, 4281-4292.  
  10419947 R.Santos, S.Bocquet, A.Puppo, and D.Touati (1999).
Characterization of an atypical superoxide dismutase from Sinorhizobium meliloti.
  J Bacteriol, 181, 4509-4516.  
9712831 M.M.Whittaker, and J.W.Whittaker (1998).
A glutamate bridge is essential for dimer stability and metal selectivity in manganese superoxide dismutase.
  J Biol Chem, 273, 22188-22193.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.