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PDBsum entry 1a8l
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Oxidoreductase PDB id
1a8l

 

 

 

 

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Contents
Protein chain
226 a.a. *
Metals
_ZN
Waters ×139
* Residue conservation analysis
PDB id:
1a8l
Name: Oxidoreductase
Title: Protein disulfide oxidoreductase from archaeon pyrococcus furiosus
Structure: Protein disulfide oxidoreductase. Chain: a. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.192     R-free:   0.217
Authors: B.Ren,G.Tibbelin,D.Pascale,M.Rossi,S.Bartolucci,R.Ladenstein
Key ref:
B.Ren et al. (1998). A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units. Nat Struct Biol, 5, 602-611. PubMed id: 9665175 DOI: 10.1038/862
Date:
26-Mar-98     Release date:   30-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q51760  (Q51760_9EURY) -  Glutaredoxin-like protein from Pyrococcus furiosus
Seq:
Struc: 		226 a.a.
226 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1038/862 Nat Struct Biol 5:602-611 (1998)
PubMed id: 9665175  
 
 
A protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus contains two thioredoxin fold units.
B.Ren, G.Tibbelin, D.de Pascale, M.Rossi, S.Bartolucci, R.Ladenstein.
 
  ABSTRACT  
 
Protein disulfide bond formation is a rate limiting step in protein folding and is catalyzed by enzymes belonging to the protein disulfide oxidoreductase superfamily, including protein disulfide isomerase (PDI) in eucarya and DsbA in bacteria. The first high resolution X-ray crystal structure of a protein disulfide oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus reveals structural details that suggest a relation to eukaryotic PDI. The protein consists of two homologous structural units with low sequence identity. Each unit contains a thioredoxin fold with a distinct CXXC active site motif. The accessibilities of both active sites are rather different as are, very likely, their redox properties. The protein shows the ability to catalyze the oxidation of dithiols as well as the reduction of disulfide bridges.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. , The final (2F[o] - F[c]) electron density maps at the active site regions of a, the N-unit and b, the C-unit. The conformation of the 14-membered disulfide ring is more relaxed in the C-unit than in the N-unit. The atoms in the C-terminal disulfide have better defined and more spherically shaped electron densities than those in the N-terminal disulfide. Both maps are contoured at the 1.2 level. 		Figure 6.
Figure 6. Fig 6 a, The coordination geometry of the zinc binding site at the dimer interface. The zinc ion is represented by a green sphere and waters by red spheres. The structural elements in the two monomers are colored in brown and blue respectively. The C-terminal end of helix 1 is distorted by forming a 3[10]-helix. The coordination angles subtended by the zinc and ligated atoms are in the range of 99−117°. b, Ribbon diagram of the pf PDO dimer. The two monomers are colored in brown and blue respectively. The active site disulfides are shown in ball-and-stick representation and colored in yellow. The two zinc ions, which are related by the crystallographic two-fold axis, are shown by green spheres.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 602-611) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20694261 A.Scirè, E.Pedone, A.Ausili, M.Saviano, M.Baldassarre, E.Bertoli, S.Bartolucci, and F.Tanfani (2010).
High hydrostatic pressure-induced conformational changes in protein disulfide oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus. A Fourier-transform infrared spectroscopic study.
  Mol Biosyst, 6, 2015-2022.  
20625793 E.Pedone, D.Limauro, K.D'Ambrosio, G.De Simone, and S.Bartolucci (2010).
Multiple catalytically active thioredoxin folds: a winning strategy for many functions.
  Cell Mol Life Sci, 67, 3797-3814.  
20598080 H.Yang, G.L.Lipscomb, A.M.Keese, G.J.Schut, M.Thomm, M.W.Adams, B.C.Wang, and R.A.Scott (2010).
SurR regulates hydrogen production in Pyrococcus furiosus by a sulfur-dependent redox switch.
  Mol Microbiol, 77, 1111-1122.  
19459661 A.Hall, D.Parsonage, D.Horita, P.A.Karplus, L.B.Poole, and E.Barbar (2009).
Redox-dependent dynamics of a dual thioredoxin fold protein: evolution of specialized folds.
  Biochemistry, 48, 5984-5993.  
18988690 D.Limauro, M.Saviano, I.Galdi, M.Rossi, S.Bartolucci, and E.Pedone (2009).
Sulfolobus solfataricus protein disulphide oxidoreductase: insight into the roles of its redox sites.
  Protein Eng Des Sel, 22, 19-26.  
19017274 G.L.Lipscomb, A.M.Keese, D.M.Cowart, G.J.Schut, M.Thomm, M.W.Adams, and R.A.Scott (2009).
SurR: a transcriptional activator and repressor controlling hydrogen and elemental sulphur metabolism in Pyrococcus furiosus.
  Mol Microbiol, 71, 332-349.  
17956189 E.Pedone, D.Limauro, and S.Bartolucci (2008).
The machinery for oxidative protein folding in thermophiles.
  Antioxid Redox Signal, 10, 157-170.  
18513746 N.P.King, T.M.Lee, M.R.Sawaya, D.Cascio, and T.O.Yeates (2008).
Structures and functional implications of an AMP-binding cystathionine beta-synthase domain protein from a hyperthermophilic archaeon.
  J Mol Biol, 380, 181-192.
PDB codes: 2rif 2rih
17508126 R.Ladenstein, and B.Ren (2008).
Reconsideration of an early dogma, saying "there is no evidence for disulfide bonds in proteins from archaea".
  Extremophiles, 12, 29-38.  
17726569 A.Becerra, L.Delaye, A.Lazcano, and L.E.Orgel (2007).
Protein disulfide oxidoreductases and the evolution of thermophily: was the last common ancestor a heat-loving microbe?
  J Mol Evol, 65, 296-303.  
17933514 B.Heras, M.Kurz, S.R.Shouldice, and J.L.Martin (2007).
The name's bond......disulfide bond.
  Curr Opin Struct Biol, 17, 691-698.  
17597419 S.Islas, R.Hernández-Morales, and A.Lazcano (2007).
Question 7: comparative genomics and early cell evolution: a cautionary methodological note.
  Orig Life Evol Biosph, 37, 415-418.  
16896527 T.Kuroita, T.Kanno, A.Kawai, B.Kawakami, M.Oka, Y.Endo, and Y.Tozawa (2007).
Functional similarities of a thermostable protein-disulfide oxidoreductase identified in the archaeon Pyrococcus horikoshii to bacterial DsbA enzymes.
  Extremophiles, 11, 85-94.  
17076700 E.Pedone, D.Limauro, R.D'Alterio, M.Rossi, and S.Bartolucci (2006).
Characterization of a multifunctional protein disulfide oxidoreductase from Sulfolobus solfataricus.
  FEBS J, 273, 5407-5420.  
16930136 R.Ladenstein, and B.Ren (2006).
Protein disulfides and protein disulfide oxidoreductases in hyperthermophiles.
  FEBS J, 273, 4170-4185.  
16677078 S.Mkrtchian, and T.Sandalova (2006).
ERp29, an unusual redox-inactive member of the thioredoxin family.
  Antioxid Redox Signal, 8, 325-337.  
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.
  Microbiol Mol Biol Rev, 69, 393-425.  
  16511034 K.D'Ambrosio, G.De Simone, E.Pedone, M.Rossi, S.Bartolucci, and C.Pedone (2005).
Crystallization and preliminary X-ray diffraction studies of a protein disulfide oxidoreductase from Aeropyrum pernix K1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 335-336.  
16111437 M.Beeby, B.D.O'Connor, C.Ryttersgaard, D.R.Boutz, L.J.Perry, and T.O.Yeates (2005).
The genomics of disulfide bonding and protein stabilization in thermophiles.
  PLoS Biol, 3, e309.
PDB code: 1rki
15601718 M.V.Weinberg, G.J.Schut, S.Brehm, S.Datta, and M.W.Adams (2005).
Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins.
  J Bacteriol, 187, 336-348.  
15291821 E.Pedone, B.Ren, R.Ladenstein, M.Rossi, and S.Bartolucci (2004).
Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus: a member of a novel protein family related to protein disulfide-isomerase.
  Eur J Biochem, 271, 3437-3448.  
15502332 K.D'Ambrosio, G.De Simone, E.Pedone, M.Rossi, S.Bartolucci, and C.Pedone (2004).
Crystallization and preliminary X-ray diffraction studies of a protein disulfide oxidoreductase from Aquifex aeolicus.
  Acta Crystallogr D Biol Crystallogr, 60, 2076-2077.  
13678529 E.A.Kersteen, and R.T.Raines (2003).
Catalysis of protein folding by protein disulfide isomerase and small-molecule mimics.
  Antioxid Redox Signal, 5, 413-424.  
12952960 J.F.Collet, J.C.D'Souza, U.Jakob, and J.C.Bardwell (2003).
Thioredoxin 2, an oxidative stress-induced protein, contains a high affinity zinc binding site.
  J Biol Chem, 278, 45325-45332.  
12121652 M.A.Edeling, L.W.Guddat, R.A.Fabianek, L.Thöny-Meyer, and J.L.Martin (2002).
Structure of CcmG/DsbE at 1.14 A resolution: high-fidelity reducing activity in an indiscriminately oxidizing environment.
  Structure, 10, 973-979.
PDB code: 1kng
11939770 S.Bhattacharyya, B.Habibi-Nazhad, G.Amegbey, C.M.Slupsky, A.Yee, C.Arrowsmith, and D.S.Wishart (2002).
Identification of a novel archaebacterial thioredoxin: determination of function through structure.
  Biochemistry, 41, 4760-4770.
PDB code: 1ilo
11551792 A.Karshikoff, and R.Ladenstein (2001).
Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads.
  Trends Biochem Sci, 26, 550-556.  
11435111 E.Liepinsh, M.Baryshev, A.Sharipo, M.Ingelman-Sundberg, G.Otting, and S.Mkrtchian (2001).
Thioredoxin fold as homodimerization module in the putative chaperone ERp29: NMR structures of the domains and experimental model of the 51 kDa dimer.
  Structure, 9, 457-471.
PDB codes: 1g7d 1g7e
11300769 Z.A.Wood, L.B.Poole, and P.A.Karplus (2001).
Structure of intact AhpF reveals a mirrored thioredoxin-like active site and implies large domain rotations during catalysis.
  Biochemistry, 40, 3900-3911.
PDB code: 1hyu
11006541 K.J.Woycechowsky, and R.T.Raines (2000).
Native disulfide bond formation in proteins.
  Curr Opin Chem Biol, 4, 533-539.  
10828978 L.B.Poole, A.Godzik, A.Nayeem, and J.D.Schmitt (2000).
AhpF can be dissected into two functional units: tandem repeats of two thioredoxin-like folds in the N-terminus mediate electron transfer from the thioredoxin reductase-like C-terminus to AhpC.
  Biochemistry, 39, 6602-6615.  
  10585970 A.J.Macario, M.Lange, B.K.Ahring, and E.C.De Macario (1999).
Stress genes and proteins in the archaea.
  Microbiol Mol Biol Rev, 63, 923.  
10361094 C.A.Orengo, A.E.Todd, and J.M.Thornton (1999).
From protein structure to function.
  Curr Opin Struct Biol, 9, 374-382.  
10464297 M.S.Alphey, G.A.Leonard, D.G.Gourley, E.Tetaud, A.H.Fairlamb, and W.N.Hunter (1999).
The high resolution crystal structure of recombinant Crithidia fasciculata tryparedoxin-I.
  J Biol Chem, 274, 25613-25622.
PDB code: 1qk8
10329642 R.T.Miller, P.Martásek, C.S.Raman, and B.S.Masters (1999).
Zinc content of Escherichia coli-expressed constitutive isoforms of nitric-oxide synthase. Enzymatic activity and effect of pterin.
  J Biol Chem, 274, 14537-14540.  
9665162 R.B.Freedman (1998).
Novel disulfide oxidoreductase in search of a function.
  Nat Struct Biol, 5, 531-532.  
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.

 

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