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PDBsum entry 1i0h

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1i0h
Jmol
Contents
Protein chains
205 a.a. *
Metals
_MN ×2
Waters ×500
* Residue conservation analysis
PDB id:
1i0h
Name: Oxidoreductase
Title: Crystal structure of the e. Coli manganese superoxide dismutase mutant y174f at 1.35 angstroms resolution.
Structure: Manganese superoxide dismutase y174f mutant. Chain: a, b. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.35Å     R-factor:   0.170     R-free:   0.196
Authors: R.A.Edwards,M.M.Whittaker,J.W.Whittaker,E.N.Baker, G.B.Jameson
Key ref:
R.A.Edwards et al. (2001). Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity. Biochemistry, 40, 4622-4632. PubMed id: 11294629 DOI: 10.1021/bi002403h
Date:
29-Jan-01     Release date:   28-Feb-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00448  (SODM_ECOLI) -  Superoxide dismutase [Mn]
Seq:
Struc:
206 a.a.
205 a.a.*
Key:    PfamA domain  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     cytoplasm   1 term 
  Biological process     cellular response to selenium ion   7 terms 
  Biochemical function     antioxidant activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi002403h Biochemistry 40:4622-4632 (2001)
PubMed id: 11294629  
 
 
Removing a hydrogen bond in the dimer interface of Escherichia coli manganese superoxide dismutase alters structure and reactivity.
R.A.Edwards, M.M.Whittaker, J.W.Whittaker, E.N.Baker, G.B.Jameson.
 
  ABSTRACT  
 
Among manganese superoxide dismutases, residues His30 and Tyr174 are highly conserved, forming part of the substrate access funnel in the active site. These two residues are structurally linked by a strong hydrogen bond between His30 NE2 from one subunit and Tyr174 OH from the other subunit of the dimer, forming an important element that bridges the dimer interface. Mutation of either His30 or Tyr174 in Escherichia coli MnSOD reduces the superoxide dismutase activity to 30--40% of that of the wt enzyme, which is surprising, since Y174 is quite remote from the active site metal center. The 2.2 A resolution X-ray structure of H30A-MnSOD shows that removing the Tyr174-->His30 hydrogen bond from the acceptor side results in a significant displacement of the main-chain segment containing the Y174 residue, with local rearrangement of the protein. The 1.35 A resolution structure of Y174F-MnSOD shows that disruption of the same hydrogen bond from the donor side has much greater consequences, with reorientation of F174 having a domino effect on the neighboring residues, resulting in a major rearrangement of the dimer interface and flipping of the His30 ring. Spectroscopic studies on H30A, H30N, and Y174F mutants show that (like the previously characterized Y34F mutant of E. coli MnSOD) all lack the high pH transition of the wt enzyme. This observation supports assignment of the pH sensitivity of MnSOD to coordination of hydroxide ion at high pH rather than to ionization of the phenolic group of Y34. Thus, mutations near the active site, as in the Y34F mutant, as well as at remote positions, as in Y174F, similarly affect the metal reactivity and alter the effective pK(a) for hydroxide ion binding. These results imply that hydrogen bonding of the H30 imidazole N--H group plays a key role in substrate binding and catalysis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18841998 M.M.Whittaker, and J.W.Whittaker (2008).
Conformationally gated metal uptake by apomanganese superoxide dismutase.
  Biochemistry, 47, 11625-11636.  
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.  
17701241 A.Stirpe, L.Sportelli, H.Wijma, M.P.Verbeet, and R.Guzzi (2007).
Thermal stability effects of removing the type-2 copper ligand His306 at the interface of nitrite reductase subunits.
  Eur Biophys J, 36, 805-813.  
  16582477 R.J.Dennis, E.Micossi, J.McCarthy, E.Moe, E.J.Gordon, S.Kozielski-Stuhrmann, G.A.Leonard, and S.McSweeney (2006).
Structure of the manganese superoxide dismutase from Deinococcus radiodurans in two crystal forms.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 325-329.
PDB codes: 2cdy 2ce4
15659371 I.G.Muñoz, J.F.Moran, M.Becana, and G.Montoya (2005).
The crystal structure of an eukaryotic iron superoxide dismutase suggests intersubunit cooperation during catalysis.
  Protein Sci, 14, 387-394.
PDB code: 1unf
14638684 A.S.Hearn, L.Fan, J.R.Lepock, J.P.Luba, W.B.Greenleaf, D.E.Cabelli, J.A.Tainer, H.S.Nick, and D.N.Silverman (2004).
Amino acid substitution at the dimeric interface of human manganese superoxide dismutase.
  J Biol Chem, 279, 5861-5866.
PDB codes: 1pl4 1pm9
14672935 R.Wintjens, C.Noël, A.C.May, D.Gerbod, F.Dufernez, M.Capron, E.Viscogliosi, and M.Rooman (2004).
Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons.
  J Biol Chem, 279, 9248-9254.  
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.  
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.