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PDBsum entry 2aps

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protein metals Protein-protein interface(s) links
Superoxide dismutase PDB id
2aps
Jmol
Contents
Protein chains
155 a.a. *
Metals
_CU ×4
_ZN ×2
Waters ×126
* Residue conservation analysis
PDB id:
2aps
Name: Superoxide dismutase
Title: Cu/zn superoxide dismutase from actinobacillus pleuropneumoniae
Structure: Protein (cu,zn superoxide dismutase). Chain: a, b. Synonym: sod. Engineered: yes. Other_details: each active site contains one copper and one zinc.
Source: Actinobacillus pleuropneumoniae. Organism_taxid: 715. Cellular_location: periplasm. Gene: sodc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.221     R-free:   0.261
Authors: K.T.Forest,P.R.Langford,J.S.Kroll,E.D.Getzoff
Key ref:
K.T.Forest et al. (2000). Cu,Zn superoxide dismutase structure from a microbial pathogen establishes a class with a conserved dimer interface. J Mol Biol, 296, 145-153. PubMed id: 10656823 DOI: 10.1006/jmbi.1999.3448
Date:
11-Feb-99     Release date:   25-Feb-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P24702  (SODC_ACTPL) -  Superoxide dismutase [Cu-Zn]
Seq:
Struc:
190 a.a.
155 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!
  Cellular component     periplasmic space   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     antioxidant activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1999.3448 J Mol Biol 296:145-153 (2000)
PubMed id: 10656823  
 
 
Cu,Zn superoxide dismutase structure from a microbial pathogen establishes a class with a conserved dimer interface.
K.T.Forest, P.R.Langford, J.S.Kroll, E.D.Getzoff.
 
  ABSTRACT  
 
Macrophages and neutrophils protect animals from microbial infection in part by issuing a burst of toxic superoxide radicals when challenged. To counteract this onslaught, many Gram-negative bacterial pathogens possess periplasmic Cu,Zn superoxide dismutases (SODs), which act on superoxide to yield molecular oxygen and hydrogen peroxide. We have solved the X-ray crystal structure of the Cu,Zn SOD from Actinobacillus pleuropneumoniae, a major porcine pathogen, by molecular replacement at 1.9 A resolution. The structure reveals that the dimeric bacterial enzymes form a structurally homologous class defined by a water-mediated dimer interface, and share with all Cu,Zn SODs the Greek-key beta-barrel subunit fold with copper and zinc ions located at the base of a deep loop-enclosed active-site channel. Our structure-based sequence alignment of the bacterial enzymes explains the monomeric nature of at least two of these, and suggests that there may be at least one additional structural class for the bacterial SODs. Two metal-mediated crystal contacts yielded our C222(1) crystals, and the geometry of these sites could be engineered into proteins recalcitrant to crystallization in their native form. This work highlights structural differences between eukaryotic and prokaryotic Cu,Zn SODs, as well as similarities and differences among prokaryotic SODs, and lays the groundwork for development of antimicrobial drugs that specifically target periplasmic Cu,Zn SODs of bacterial pathogens.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The overall structure of A. pleuropneumoniae SOD (ApSOD). (a) Schematic diagram of ApSOD subunit connectivity. The eight antiparallel b-strands are numbered based on their three-dimensional order of appearance around the b-barrel, and the sequence order is indicated with lower-case letters. The connections are afforded by a Greek-key loop from b3c to b6d and a Greek-key helix from b4f to b7g. Extra-barrel loops form the metal-containing active-site and the electrostatic attraction loop. (b) C a trace of the SOD dimer, colored by thermal factor (gradual change from dark blue <20 Å 2 to red >95 Å 2 ), shows that the disorder is much higher in Sub(unit)1, in particular the extended loops from residues 20-25 and 70-75 (upper right). These loops border the large solvent channel in the crys- tals, whereas in Sub2, the loops form crystal contacts with a neighboring molecule and are well-ordered, with no ambiguity in the interpretation of the map. (c) Schematic ribbon rendering of the molecule showing dimer interface side-chains (green) and water molecules (red) as well as the disulfide bond (yellow) and metals (orange sphere, cop- per and silver sphere, zinc) and side-chains in the active-site (colored by atom type). Interface water molecules obey the non-crystallographic 2-fold symmetry. The charged residues (orange side-chains, top left, shown only for Sub2) at the tip of the electrostatic loop, together with the catalytic copper, form an electrostatically favorable pathway for substrate superoxide ions. The active-site channel is formed between loops on the side of the b-barrel. Copper ligands His60 N d1 , His62 N e2 , and His141 N e2 are 1.99-2.13 Å from the Cu(II) ion, which is exposed at the bottom of the active-site channel. The structural zinc is buried 6.4 Å under the copper and ligated by His85 N d1 , His94 N d1 , His103 N d1 and Asp106 O d1 , with bond distances of 2.00 Å for the Asp residue and 2.07-2.12 Å for the histidine residues.
Figure 2.
Figure 2. Water-mediated dimer interface and copper-mediated crystal contacts. (a) The ring of conserved waters (red crosses) in a stereo view of a 5 Å slab of the final 2Fo - Fc electron density map (green basketweave, contoured at 1.0 s). This view is rotated 90 ° around the vertical 2-fold axis from that shown in Figure 1(c), so that the two Trp98 side-chains are across from each other rather than one in front of the other. (b) A schematic of the hydrogen- bonding network in the dimer interface. In an example water-mediated interaction, the carbonyl oxygen atom of Ala109 is hydrogen-bonded to water molecule 1244, which is itself further hydrogen bonded to the side-chain of Asn120 in the second subunit of the same SOD dimer. This view, although schematic, is similar to that shown in Figure 1(c). (c) Cu 300 lies on a special position and forms a crystal contact between symmetry-related 2-fold Sub1s via His48 and His50. Electron density is contoured at 1 s (green) and 5 s (gold) above the mean.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 296, 145-153) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19063897 D.S.Shin, M.Didonato, D.P.Barondeau, G.L.Hura, C.Hitomi, J.A.Berglund, E.D.Getzoff, S.C.Cary, and J.A.Tainer (2009).
Superoxide dismutase from the eukaryotic thermophile Alvinella pompejana: structures, stability, mechanism, and insights into amyotrophic lateral sclerosis.
  J Mol Biol, 385, 1534-1555.
PDB codes: 3f7k 3f7l
18645238 M.Yogavel, P.C.Mishra, J.Gill, P.K.Bhardwaj, S.Dutt, S.Kumar, P.S.Ahuja, and A.Sharma (2008).
Structure of a superoxide dismutase and implications for copper-ion chelation.
  Acta Crystallogr D Biol Crystallogr, 64, 892-901.  
17416645 R.Krishnakumar, B.Kim, E.A.Mollo, J.A.Imlay, and J.M.Slauch (2007).
Structural properties of periplasmic SodCI that correlate with virulence in Salmonella enterica serovar Typhimurium.
  J Bacteriol, 189, 4343-4352.  
16988021 W.W.Fung, C.A.O'Dwyer, S.Sinha, A.L.Brauer, T.F.Murphy, J.S.Kroll, and P.R.Langford (2006).
Presence of copper- and zinc-containing superoxide dismutase in commensal Haemophilus haemolyticus isolates can be used as a marker to discriminate them from nontypeable H. influenzae isolates.
  J Clin Microbiol, 44, 4222-4226.  
15897454 L.Banci, I.Bertini, V.Calderone, F.Cramaro, R.Del Conte, A.Fantoni, S.Mangani, A.Quattrone, and M.S.Viezzoli (2005).
A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal.
  Proc Natl Acad Sci U S A, 102, 7541-7546.
PDB codes: 1s4i 1u3n
15333927 R.M.Cardoso, C.H.Silva, A.P.Ulian de Araújo, T.Tanaka, M.Tanaka, and R.C.Garratt (2004).
Structure of the cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni.
  Acta Crystallogr D Biol Crystallogr, 60, 1569-1578.
PDB codes: 1to4 1to5
11849539 S.S.Korshunov, and J.A.Imlay (2002).
A potential role for periplasmic superoxide dismutase in blocking the penetration of external superoxide into the cytosol of Gram-negative bacteria.
  Mol Microbiol, 43, 95.  
11679732 W.Liu, P.W.Li, G.P.Li, R.H.Zhu, and D.C.Wang (2001).
Overexpression, purification, crystallization and preliminary X-ray diffraction analysis of Cu,Zn superoxide dismutase from Peking duck.
  Acta Crystallogr D Biol Crystallogr, 57, 1646-1649.  
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.