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PDBsum entry 1e0c

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protein ligands metals links
Sulfurtransferase PDB id
1e0c
Jmol PyMol
Contents
Protein chain
271 a.a. *
Ligands
SO4 ×2
EDO ×2
Metals
_MG ×3
Waters ×341
* Residue conservation analysis
PDB id:
1e0c
Name: Sulfurtransferase
Title: Sulfurtransferase from azotobacter vinelandii
Structure: Sulfurtransferase. Chain: a. Synonym: rhodanese. Engineered: yes
Source: Azotobacter vinelandii. Organism_taxid: 354. Cellular_location: cytoplasm. Gene: rhda. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: pre4. Other_details: synthetic gene
Resolution:
1.8Å     R-factor:   0.180     R-free:   0.230
Authors: D.Bordo,D.Deriu,R.Colnaghi,A.Carpen,S.Pagani,M.Bolognesi
Key ref:
D.Bordo et al. (2000). The crystal structure of a sulfurtransferase from Azotobacter vinelandii highlights the evolutionary relationship between the rhodanese and phosphatase enzyme families. J Mol Biol, 298, 691-704. PubMed id: 10788330 DOI: 10.1006/jmbi.2000.3651
Date:
23-Mar-00     Release date:   08-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P52197  (THTR_AZOVI) -  Thiosulfate sulfurtransferase
Seq:
Struc:
271 a.a.
271 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.8.1.1  - Thiosulfate sulfurtransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Thiosulfate + cyanide = sulfite + thiocyanate
Thiosulfate
+ cyanide
=
sulfite
Bound ligand (Het Group name = SO4)
matches with 80.00% similarity
+ thiocyanate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biochemical function     protein binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3651 J Mol Biol 298:691-704 (2000)
PubMed id: 10788330  
 
 
The crystal structure of a sulfurtransferase from Azotobacter vinelandii highlights the evolutionary relationship between the rhodanese and phosphatase enzyme families.
D.Bordo, D.Deriu, R.Colnaghi, A.Carpen, S.Pagani, M.Bolognesi.
 
  ABSTRACT  
 
Rhodanese is an ubiquitous enzyme that in vitro catalyses the transfer of a sulfur atom from suitable donors to nucleophilic acceptors by way of a double displacement mechanism. During the catalytic process the enzyme cycles between a sulfur-free and a persulfide-containing form, via formation of a persulfide linkage to a catalytic Cys residue. In the nitrogen-fixing bacteria Azotobacter vinelandii the rhdA gene has been identified and the encoded protein functionally characterized as a rhodanese. The crystal structure of the A. vinelandii rhodanese has been determined and refined at 1.8 A resolution in the sulfur-free and persulfide-containing forms. Conservation of the overall three-dimensional fold of bovine rhodanese is observed, with substantial modifications of the protein structure in the proximity of the catalytic residue Cys230. Remarkably, the native enzyme is found as the Cys230-persulfide form; in the sulfur-free state the catalytic Cys residue adopts two alternate conformations, reflected by perturbation of the neighboring active-site residues, which is associated with a partly reversible loss of thiosulfate:cyanide sulfurtransferase activity. The catalytic mechanism of A. vinelandii rhodanese relies primarily on the main-chain conformation of the 230 to 235 active-site loop and on a surrounding strong positive electrostatic field. Substrate recognition is based on residues which are entirely different in the prokaryotic and eukaryotic enzymes. The active-site loop of A. vinelandii rhodanese displays striking structural similarity to the active-site loop of the similarly folded catalytic domain of dual specific phosphatase Cdc25, suggesting a common evolutionary origin of the two enzyme families.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Overall structure of A. vinelandii rhodanese. (a) Stereoview of the C^a trace, with the molecular pseudo 2-fold axis approximately normal to the plane of the image. (b) Ribbon representation of RhdA. The N- and C-terminal domains (brown and green, respectively), the linker peptide (blue). The secondary structure elements of each domain are labeled with letters following the scheme proposed for bovine rhodanese [Ploegman et al 1978]. A single quote indicates elements of the C-terminal domains. The active-site loop is shown in red; the catalytic residue, Cys230, is represented in ball and stick. The drawings were prepared with the programs MOLSCRIPT [Kraulis 1991] and Raster3D [Merrit and Murphy 1994].
Figure 3.
Figure 3. Stereo representation of the active-site environment of the sulfur-free rhodanese. The alternate conformations of Cys230, Arg235, and Trp195 side-chains are shown in grey and green, respectively; hydrogen bonds as red dotted lines.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 298, 691-704) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20213443 F.Cartini, W.Remelli, P.C.Dos Santos, J.Papenbrock, S.Pagani, and F.Forlani (2011).
Mobilization of sulfane sulfur from cysteine desulfurases to the Azotobacter vinelandii sulfurtransferase RhdA.
  Amino Acids, 41, 141-150.  
20135153 J.Papenbrock, S.Guretzki, and M.Henne (2011).
Latest news about the sulfurtransferase protein family of higher plants.
  Amino Acids, 41, 43-57.  
20404999 R.Shi, A.Proteau, M.Villarroya, I.Moukadiri, L.Zhang, J.F.Trempe, A.Matte, M.E.Armengod, and M.Cygler (2010).
Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions.
  PLoS Biol, 8, e1000354.
PDB codes: 3lvj 3lvk 3lvl 3lvm
20482308 W.Remelli, A.Cereda, J.Papenbrock, F.Forlani, and S.Pagani (2010).
The rhodanese RhdA helps Azotobacter vinelandii in maintaining cellular redox balance.
  Biol Chem, 391, 777-784.  
19382206 H.K.Yeo, and J.Y.Lee (2009).
Crystal structure of Saccharomyces cerevisiae Ygr203w, a homolog of single-domain rhodanese and Cdc25 phosphatase catalytic domain.
  Proteins, 76, 520-524.
PDB code: 3fs5
19725515 J.R.Wallen, T.C.Mallett, W.Boles, D.Parsonage, C.M.Furdui, P.A.Karplus, and A.Claiborne (2009).
Crystal structure and catalytic properties of Bacillus anthracis CoADR-RHD: implications for flavin-linked sulfur trafficking.
  Biochemistry, 48, 9650-9667.
PDB codes: 3icr 3ics 3ict
19798741 P.Hänzelmann, J.U.Dahl, J.Kuper, A.Urban, U.Müller-Theissen, S.Leimkühler, and H.Schindelin (2009).
Crystal structure of YnjE from Escherichia coli, a sulfurtransferase with three rhodanese domains.
  Protein Sci, 18, 2480-2491.
PDB codes: 3ipo 3ipp
  19088907 H.Cheng, J.L.Donahue, S.E.Battle, W.K.Ray, and T.J.Larson (2008).
Biochemical and Genetic Characterization of PspE and GlpE, Two Single-domain Sulfurtransferases of Escherichia coli.
  Open Microbiol J, 2, 18-28.  
18616471 R.Sabelli, E.Iorio, A.De Martino, F.Podo, A.Ricci, G.Viticchiè, G.Rotilio, M.Paci, and S.Melino (2008).
Rhodanese-thioredoxin system and allyl sulfur compounds.
  FEBS J, 275, 3884-3899.  
17214549 A.Bartels, F.Forlani, S.Pagani, and J.Papenbrock (2007).
Conformational studies on Arabidopsis sulfurtransferase AtStr1 with spectroscopic methods.
  Biol Chem, 388, 53-59.  
17109059 L.Cavalca, N.Guerrieri, M.Colombo, S.Pagani, and V.Andreoni (2007).
Enzymatic and genetic profiles in environmental strains grown on polycyclic aromatic hydrocarbons.
  Antonie Van Leeuwenhoek, 91, 315-325.  
17697123 M.C.Giuliani, P.Tron, G.Leroy, C.Aubert, P.Tauc, and M.T.Giudici-Orticoni (2007).
A new sulfurtransferase from the hyperthermophilic bacterium Aquifex aeolicus. Being single is not so simple when temperature gets high.
  FEBS J, 274, 4572-4587.  
17522046 V.Sauvé, S.Bruno, B.C.Berks, and A.M.Hemmings (2007).
The SoxYZ complex carries sulfur cycle intermediates on a peptide swinging arm.
  J Biol Chem, 282, 23194-23204.
PDB codes: 2ox5 2oxg 2oxh
17400920 X.Tao, and L.Tong (2007).
Crystal structure of the MAP kinase binding domain and the catalytic domain of human MKP5.
  Protein Sci, 16, 880-886.
PDB codes: 2ouc 2oud
  17012788 D.Bisacchi, Y.Zhou, B.P.Rosen, R.Mukhopadhyay, and D.Bordo (2006).
Crystallization and preliminary crystallographic characterization of LmACR2, an arsenate/antimonate reductase from Leishmania major.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 976-979.  
16680676 M.Hattori, E.Mizohata, A.Tatsuguchi, R.Shibata, S.Kishishita, K.Murayama, T.Terada, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2006).
Crystal structure of the single-domain rhodanese homologue TTHA0613 from Thermus thermophilus HB8.
  Proteins, 64, 284-287.
PDB code: 1wv9
16484493 T.Urich, C.M.Gomes, A.Kletzin, and C.Frazão (2006).
X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme.
  Science, 311, 996.
PDB code: 2cb2
17136732 Z.Prokop, F.Oplustil, J.DeFrank, and J.Damborský (2006).
Enzymes fight chemical weapons.
  Biotechnol J, 1, 1370-1380.  
15576557 D.Pantoja-Uceda, B.López-Méndez, S.Koshiba, M.Inoue, T.Kigawa, T.Terada, M.Shirouzu, A.Tanaka, M.Seki, K.Shinozaki, S.Yokoyama, and P.Güntert (2005).
Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana.
  Protein Sci, 14, 224-230.
PDB code: 1vee
16008502 K.S.Carroll, H.Gao, H.Chen, C.D.Stout, J.A.Leary, and C.R.Bertozzi (2005).
A conserved mechanism for sulfonucleotide reduction.
  PLoS Biol, 3, e250.  
15805776 M.Acosta, S.Beard, J.Ponce, M.Vera, J.C.Mobarec, and C.A.Jerez (2005).
Identification of putative sulfurtransferase genes in the extremophilic Acidithiobacillus ferrooxidans ATCC 23270 genome: structural and functional characterization of the proteins.
  OMICS, 9, 13-29.  
14669990 A.Cereda, F.Forlani, S.Iametti, R.Bernhardt, P.Ferranti, G.Picariello, S.Pagani, and F.Bonomi (2003).
Molecular recognition between Azotobacter vinelandii rhodanese and a sulfur acceptor protein.
  Biol Chem, 384, 1473-1481.  
12419809 R.A.Williams, S.M.Kelly, J.C.Mottram, and G.H.Coombs (2003).
3-Mercaptopyruvate sulfurtransferase of Leishmania contains an unusual C-terminal extension and is involved in thioredoxin and antioxidant metabolism.
  J Biol Chem, 278, 1480-1486.  
14519133 S.Melino, D.O.Cicero, M.Orsale, F.Forlani, S.Pagani, and M.Paci (2003).
Azotobacter vinelandii rhodanese: selenium loading and ion interaction studies.
  Eur J Biochem, 270, 4208-4215.  
12377129 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Sequence and structural differences between enzyme and nonenzyme homologs.
  Structure, 10, 1435-1451.  
12151332 D.Bordo, and P.Bork (2002).
The rhodanese/Cdc25 phosphatase superfamily. Sequence-structure-function relations.
  EMBO Rep, 3, 741-746.  
12437129 M.Burow, D.Kessler, and J.Papenbrock (2002).
Enzymatic activity of the Arabidopsis sulfurtransferase resides in the C-terminal domain but is boosted by the N-terminal domain and the linker peptide in the full-length enzyme.
  Biol Chem, 383, 1363-1372.  
12411478 V.A.Bamford, S.Bruno, T.Rasmussen, C.Appia-Ayme, M.R.Cheesman, B.C.Berks, and A.M.Hemmings (2002).
Structural basis for the oxidation of thiosulfate by a sulfur cycle enzyme.
  EMBO J, 21, 5599-5610.
PDB codes: 1h31 1h32 1h33
11709175 A.Spallarossa, J.L.Donahue, T.J.Larson, M.Bolognesi, and D.Bordo (2001).
Escherichia coli GlpE is a prototype sulfurtransferase for the single-domain rhodanese homology superfamily.
  Structure, 9, 1117-1125.
PDB codes: 1gmx 1gn0
11592406 D.Bordo, F.Forlani, A.Spallarossa, R.Colnaghi, A.Carpen, M.Bolognesi, and S.Pagani (2001).
A persulfurated cysteine promotes active site reactivity in Azotobacter vinelandii Rhodanese.
  Biol Chem, 382, 1245-1252.
PDB codes: 1h4k 1h4m
11298762 S.Iametti, A.K.Bera, G.Vecchio, A.Grinberg, R.Bernhardt, and F.Bonomi (2001).
GroEL-assisted refolding of adrenodoxin during chemical cluster insertion.
  Eur J Biochem, 268, 2421-2429.  
11092948 D.Bordo, T.J.Larson, J.L.Donahue, A.Spallarossa, and M.Bolognesi (2000).
Crystals of GlpE, a 12 kDa sulfurtransferase from escherichia coli, display 1.06 A resolution diffraction: a preliminary report.
  Acta Crystallogr D Biol Crystallogr, 56, 1691-1693.  
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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