3MDS

MAGANESE SUPEROXIDE DISMUTASE FROM THERMUS THERMOPHILUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Manganese superoxide dismutase from Thermus thermophilus. A structural model refined at 1.8 A resolution.

Ludwig, M.L.Metzger, A.L.Pattridge, K.A.Stallings, W.C.

(1991) J Mol Biol 219: 335-358

  • DOI: 10.1016/0022-2836(91)90569-r
  • Primary Citation of Related Structures:  
    3MDS

  • PubMed Abstract: 
  • The structure of Mn(III) superoxide dismutase (Mn(III)SOD) from Thermus thermophilus, a tetramer of chains 203 residues in length, has been refined by restrained least-squares methods. The R-factor [formula: see text] for the 54,056 unique reflections me ...

    The structure of Mn(III) superoxide dismutase (Mn(III)SOD) from Thermus thermophilus, a tetramer of chains 203 residues in length, has been refined by restrained least-squares methods. The R-factor [formula: see text] for the 54,056 unique reflections measured between 10.0 and 1.8 A (96% of all possible reflections) is 0.176 for a model comprising the protein dimer and 180 bound solvents, the asymmetric unit of the P4(1)2(1)2 cell. The monomer chain forms two domains as determined by distance plots: the N-terminal domain is dominated by two long antiparallel helices (residues 21 to 45 and 69 to 89) and the C-terminal domain (residues 100 to 203) is an alpha + beta structure including a three-stranded sheet. Features that may be important for the folding and function of this MnSOD include: (1) a cis-proline in a turn preceding the first long helix; (2) a residue inserted at position 30 that distorts the helix near the first Mn ligand; and (3) the locations of glycine and proline residues in the domain connector (residues 92 to 99) and in the vicinity of the short cross connection (residues 150 to 159) that links two strands of the beta-sheet. Domain-domain contacts include salt bridges between arginine residues and acidic side chains, an extensive hydrophobic interface, and at least ten hydrogen-bonded interactions. The tetramer possesses 222 symmetry but is held together by only two types of interfaces. The dimer interface at the non-crystallographic dyad is extensive (1000 A2 buried surface/monomer) and incorporates 17 trapped or structural solvents. The dimer interface at the crystallographic dyad buries fewer residues (750 A2/monomer) and resembles a snap fastener in which a type I turn thrusts into a hydrophobic basket formed by a ring of helices in the opposing chain. Each of the metal sites is fully occupied, with the Mn(III) five-co-ordinate in trigonal bipyramidal geometry. One of the axial ligands is solvent; the four protein ligands are His28, His83, Asp166 and His170. Surrounding the metal-ligand cluster is a shell of predominantly hydrophobic residues from both chains of the asymmetric unit (Phe86A, Trp87A, Trp132A, Trp168A, Tyr183A, Tyr172B, Tyr173B), and both chains collaborate in the formation of a solvent-lined channel that terminates at Tyr36 and His32 near the metal ion and is presumed to be the path by which substrate or other inner-sphere ligands reach the metal.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Iron and Manganese Superoxide Dismutases: Catalytic Inferences from the Structures Molecular Biology of Free Radical Scavenging Systems
      Stallings, W.C., Bull, C., Fee, J.A., Lah, M.S., Ludwig, M.L.
      (1992) Molecular Biology Of Free Radical Scavenging Systems --: 193
    • Structure-Function Relationships in Fe-and Mn-Superoxide Dismutases
      Stallings, W.C., Metzger, A.L., Pattridge, K.A., Fee, J.A., Ludwig, M.L.
      (1991) Free Radic Res Commun 12: 259
    • The Structure of Manganese Superoxide Dismutase from Thermus Thermophilus at 2.4 Angstroms Resolution
      Stallings, W.C., Pattridge, K.A., Strong, R.K., Ludwig, M.L.
      (1985) J Biol Chem 260: 16424
    • Manganese and Iron Superoxide Dismutases are Structural Homologs
      Stallings, W.C., Pattridge, K.A., Strong, R.K., Ludwig, M.L.
      (1984) J Biol Chem 259: 10695

    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor 48109.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANGANESE SUPEROXIDE DISMUTASE AB203Thermus thermophilusMutation(s): 0 
EC: 1.15.1.1
Find proteins for P61503 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P61503 
Go to UniProtKB:  P61503
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN3
Query on MN3

Download Ideal Coordinates CCD File 
A, B
MANGANESE (III) ION
Mn
MMIPFLVOWGHZQD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.6α = 90
b = 146.6β = 90
c = 55.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other