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PDBsum entry 3mds

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protein metals Protein-protein interface(s) links
Oxidoreductase(superoxide acceptor) PDB id
3mds
Jmol
Contents
Protein chains
203 a.a. *
Metals
MN3 ×2
Waters ×187
* Residue conservation analysis
PDB id:
3mds
Name: Oxidoreductase(superoxide acceptor)
Title: Maganese superoxide dismutase from thermus thermophilus
Structure: Manganese superoxide dismutase. Chain: a, b. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.190    
Authors: M.L.Ludwig,A.L.Metzger,K.A.Pattridge,W.C.Stallings
Key ref: M.L.Ludwig et al. (1991). Manganese superoxide dismutase from Thermus thermophilus. A structural model refined at 1.8 A resolution. J Mol Biol, 219, 335-358. PubMed id: 2038060
Date:
20-Oct-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61503  (SODM_THET8) -  Superoxide dismutase [Mn]
Seq:
Struc:
204 a.a.
203 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    Added reference    
 
 
J Mol Biol 219:335-358 (1991)
PubMed id: 2038060  
 
 
Manganese superoxide dismutase from Thermus thermophilus. A structural model refined at 1.8 A resolution.
M.L.Ludwig, A.L.Metzger, K.A.Pattridge, W.C.Stallings.
 
  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 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)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20626318 M.Gleichmann, and M.P.Mattson (2011).
Neuronal calcium homeostasis and dysregulation.
  Antioxid Redox Signal, 14, 1261-1273.  
21487935 P.Ceci, E.Forte, G.Di Cecca, M.Fornara, and E.Chiancone (2011).
The characterization of Thermotoga maritima ferritin reveals an unusual subunit dissociation behavior and efficient DNA protection from iron-mediated oxidative stress.
  Extremophiles, 15, 431-439.  
21182595 T.Nakamura, K.Torikai, K.Uegaki, J.Morita, K.Machida, A.Suzuki, and Y.Kawata (2011).
Crystal structure of the cambialistic superoxide dismutase from Aeropyrum pernix K1--insights into the enzyme mechanism and stability.
  FEBS J, 278, 598-609.
PDB codes: 3ak1 3ak2 3ak3
19707802 H.I.Lee, J.W.Lee, T.C.Yang, S.O.Kang, and B.M.Hoffman (2010).
ENDOR and ESEEM investigation of the Ni-containing superoxide dismutase.
  J Biol Inorg Chem, 15, 175-182.  
21054499 Y.Agari, S.Kuramitsu, and A.Shinkai (2010).
Identification of novel genes regulated by the oxidative stress-responsive transcriptional activator SdrP in Thermus thermophilus HB8.
  FEMS Microbiol Lett, 313, 127-134.  
19755112 M.M.Whittaker, and J.W.Whittaker (2009).
In vitro metal uptake by recombinant human manganese superoxide dismutase.
  Arch Biochem Biophys, 491, 69-74.  
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.  
  19052361 C.H.Trinh, T.Hunter, E.E.Stewart, S.E.Phillips, and G.J.Hunter (2008).
Purification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1110-1114.
PDB codes: 3dc5 3dc6
18640608 K.Isobe, A.Kato, Y.Sasaki, M.Kataoka, J.Ogawa, A.Iwasaki, J.Hasegawa, and S.Shimizu (2008).
Superoxide dismutases exhibit oxidase activity on aldehyde alcohols similar to alcohol oxidase from Paenibacillus sp. AIU 311.
  J Biosci Bioeng, 105, 666-670.  
  18084079 P.Liu, H.E.Ewis, Y.J.Huang, C.D.Lu, P.C.Tai, and I.T.Weber (2007).
Structure of Bacillus subtilis superoxide dismutase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1003-1007.
PDB code: 2rcv
17262208 Y.Z.He, K.Q.Fan, C.J.Jia, Z.J.Wang, W.B.Pan, L.Huang, K.Q.Yang, and Z.Y.Dong (2007).
Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring.
  Appl Microbiol Biotechnol, 75, 367-376.  
16242020 M.V.Omelchenko, Y.I.Wolf, E.K.Gaidamakova, V.Y.Matrosova, A.Vasilenko, M.Zhai, M.J.Daly, E.V.Koonin, and K.S.Makarova (2005).
Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.
  BMC Evol Biol, 5, 57.  
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.  
12215453 G.Regelsberger, W.Atzenhofer, F.Ruker, G.A.Peschek, C.Jakopitsch, M.Paumann, P.G.Furtmüller, and C.Obinger (2002).
Biochemical characterization of a membrane-bound manganese-containing superoxide dismutase from the cyanobacterium Anabaena PCC 7120.
  J Biol Chem, 277, 43615-43622.  
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
10704199 A.P.Yeh, Y.Hu, F.E.Jenney, M.W.Adams, and D.C.Rees (2000).
Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states.
  Biochemistry, 39, 2499-2508.
PDB codes: 1do6 1dqi 1dqk
11154067 S.Kardinahl, S.Anemüller, and G.Schäfer (2000).
The hyper-thermostable Fe-superoxide dismutase from the Archaeon Acidianus ambivalens: characterization, recombinant expression, crystallization and effects of metal exchange.
  Biol Chem, 381, 1089-1101.  
10848964 S.Sugio, B.Y.Hiraoka, and F.Yamakura (2000).
Crystal structure of cambialistic superoxide dismutase from porphyromonas gingivalis.
  Eur J Biochem, 267, 3487-3495.
PDB code: 1qnn
10514376 F.E.Jenney, M.F.Verhagen, X.Cui, and M.W.Adams (1999).
Anaerobic microbes: oxygen detoxification without superoxide dismutase.
  Science, 286, 306-309.  
10574944 M.M.Whittaker, and J.W.Whittaker (1999).
Thermally triggered metal binding by recombinant Thermus thermophilus manganese superoxide dismutase, expressed as the apo-enzyme.
  J Biol Chem, 274, 34751-34757.  
9698380 C.L.Borders, M.J.Bjerrum, M.A.Schirmer, and S.G.Oliver (1998).
Characterization of recombinant Saccharomyces cerevisiae manganese-containing superoxide dismutase and its H30A and K170R mutants expressed in Escherichia coli.
  Biochemistry, 37, 11323-11331.  
9603906 F.Yamakura, H.Taka, T.Fujimura, and K.Murayama (1998).
Inactivation of human manganese-superoxide dismutase by peroxynitrite is caused by exclusive nitration of tyrosine 34 to 3-nitrotyrosine.
  J Biol Chem, 273, 14085-14089.  
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.  
9537987 Y.Guan, M.J.Hickey, G.E.Borgstahl, R.A.Hallewell, J.R.Lepock, D.O'Connor, Y.Hsieh, H.S.Nick, D.N.Silverman, and J.A.Tainer (1998).
Crystal structure of Y34F mutant human mitochondrial manganese superoxide dismutase and the functional role of tyrosine 34.
  Biochemistry, 37, 4722-4730.
PDB codes: 1ap5 1ap6
9537988 Y.Hsieh, Y.Guan, C.Tu, P.J.Bratt, A.Angerhofer, J.R.Lepock, M.J.Hickey, J.A.Tainer, H.S.Nick, and D.N.Silverman (1998).
Probing the active site of human manganese superoxide dismutase: the role of glutamine 143.
  Biochemistry, 37, 4731-4739.
PDB code: 1qnm
9125513 D.L.Sorkin, and A.F.Miller (1997).
Spectroscopic measurement of a long-predicted active site pK in iron-superoxide dismutase from Escherichia coli.
  Biochemistry, 36, 4916-4924.  
9204864 D.L.Sorkin, D.K.Duong, and A.F.Miller (1997).
Mutation of tyrosine 34 to phenylalanine eliminates the active site pK of reduced iron-containing superoxide dismutase.
  Biochemistry, 36, 8202-8208.  
9220980 M.M.Whittaker, and J.W.Whittaker (1997).
Mutagenesis of a proton linkage pathway in Escherichia coli manganese superoxide dismutase.
  Biochemistry, 36, 8923-8931.  
9125514 T.Hunter, K.Ikebukuro, W.H.Bannister, J.V.Bannister, and G.J.Hunter (1997).
The conserved residue tyrosine 34 is essential for maximal activity of iron-superoxide dismutase from Escherichia coli.
  Biochemistry, 36, 4925-4933.  
8663465 J.L.Hsu, Y.Hsieh, C.Tu, D.O'Connor, H.S.Nick, and D.N.Silverman (1996).
Catalytic properties of human manganese superoxide dismutase.
  J Biol Chem, 271, 17687-17691.  
8643556 L.M.Carlsson, S.L.Marklund, and T.Edlund (1996).
The rat extracellular superoxide dismutase dimer is converted to a tetramer by the exchange of a single amino acid.
  Proc Natl Acad Sci U S A, 93, 5219-5222.  
8639627 M.M.Whittaker, and J.W.Whittaker (1996).
Low-temperature thermochromism marks a change in coordination for the metal ion in manganese superoxide dismutase.
  Biochemistry, 35, 6762-6770.  
8874031 S.Kumar, and M.Bansal (1996).
Structural and sequence characteristics of long alpha helices in globular proteins.
  Biophys J, 71, 1574-1586.  
7867628 F.Yamakura, K.Kobayashi, H.Ue, and M.Konno (1995).
The pH-dependent changes of the enzymic activity and spectroscopic properties of iron-substituted manganese superoxide dismutase. A study on the metal-specific activity of Mn-containing superoxide dismutase.
  Eur J Biochem, 227, 700-706.  
8527681 G.A.Landrum, C.A.Ekberg, and J.W.Whittaker (1995).
A ligand field model for MCD spectra of biological cupric complexes.
  Biophys J, 69, 674-689.  
8307013 B.Meier, A.P.Sehn, M.E.Schininà, and D.Barra (1994).
In vivo incorporation of copper into the iron-exchangeable and manganese-exchangeable superoxide dismutase from Propionibacterium shermanii. Amino acid sequence and identity of the protein moieties.
  Eur J Biochem, 219, 463-468.  
  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
  8495200 U.G.Wagner, K.A.Pattridge, M.L.Ludwig, W.C.Stallings, M.M.Werber, C.Oefner, F.Frolow, and J.L.Sussman (1993).
Comparison of the crystal structures of genetically engineered human manganese superoxide dismutase and manganese superoxide dismutase from Thermus thermophilus: differences in dimer-dimer interaction.
  Protein Sci, 2, 814-825.
PDB code: 1msd
1394426 G.E.Borgstahl, H.E.Parge, M.J.Hickey, W.F.Beyer, R.A.Hallewell, and J.A.Tainer (1992).
The structure of human mitochondrial manganese superoxide dismutase reveals a novel tetrameric interface of two 4-helix bundles.
  Cell, 71, 107-118.
PDB codes: 1abm 1n0j
1779751 J.A.Fee (1991).
Regulation of sod genes in Escherichia coli: relevance to superoxide dismutase function.
  Mol Microbiol, 5, 2599-2610.  
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.