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PDBsum entry 1dw9

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1dw9
Jmol
Contents
Protein chains
(+ 4 more) 156 a.a. *
Ligands
SO4 ×23
Metals
_CL ×10
Waters ×1865
* Residue conservation analysis
PDB id:
1dw9
Name: Lyase
Title: Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site
Structure: Cyanate lyase. Chain: a, b, c, d, e, f, g, h, i, j. Synonym: cyanate hydrolase, cyanase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Decamer (from PQS)
Resolution:
1.65Å     R-factor:   0.150     R-free:   0.189
Authors: M.A.Walsh,Z.Otwinowski,A.Perrakis,P.M.Anderson,A.Joachimiak, Center For Structural Genomics (Mcsg)
Key ref:
M.A.Walsh et al. (2000). Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. Structure, 8, 505-514. PubMed id: 10801492 DOI: 10.1016/S0969-2126(00)00134-9
Date:
03-Dec-99     Release date:   16-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00816  (CYNS_ECOLI) -  Cyanate hydratase
Seq:
Struc:
156 a.a.
156 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.104  - Cyanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cyanate + HCO3- + 2 H+ = NH3 + 2 CO2
Cyanate
+ HCO(3)(-)
+ 2 × H(+)
= NH(3)
+ 2 × CO(2)
      Cofactor: Bicarbonate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cyanate metabolic process   2 terms 
  Biochemical function     lyase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00134-9 Structure 8:505-514 (2000)
PubMed id: 10801492  
 
 
Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.
M.A.Walsh, Z.Otwinowski, A.Perrakis, P.M.Anderson, A.Joachimiak.
 
  ABSTRACT  
 
BACKGROUND: Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. RESULTS: We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. CONCLUSIONS: The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Ball-and-stick diagram showing orthogonal views of the five Arg87 cavity-bound sulfate ions in the cyanase decamer. (a) Looking down the fivefold axis. (b) Perpendicular to the fivefold axis. Residues are labeled by their sequence number and respective monomer chain, as described in Figure 4. The bound sulfate ions are labeled as K111-K115, which follows the assignment in the coordinate file 1DW9 deposited in the PDB. The arginine residues are colored blue and yellow to highlight the delineation of the monomers as above and below the equatorial b-sheet belt formed by the dimer interface domain (see Figure 3). The sulfate ions are colored by atom type (sulfur, orange; oxygen, red). (The figure was generated with Molscript [62] and rendered with Raster 3D [63].)

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 505-514) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460451 N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and R.A.de Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.
  Acta Crystallogr D Biol Crystallogr, 67, 331-337.  
20606258 P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.
  Acta Crystallogr D Biol Crystallogr, 66, 783-788.  
20179338 T.C.Terwilliger (2010).
Rapid model building of alpha-helices in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 268-275.  
20179339 T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 276-284.  
20179340 T.C.Terwilliger (2010).
Rapid chain tracing of polypeptide backbones in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 285-294.  
18645235 C.Dumas, and A.van der Lee (2008).
Macromolecular structure solution by charge flipping.
  Acta Crystallogr D Biol Crystallogr, 64, 864-873.  
18708510 V.M.Luque-Almagro, M.J.Huertas, L.P.Sáez, M.M.Luque-Romero, C.Moreno-Vivián, F.Castillo, M.D.Roldán, and R.Blasco (2008).
Characterization of the Pseudomonas pseudoalcaligenes CECT5344 Cyanase, an enzyme that is not essential for cyanide assimilation.
  Appl Environ Microbiol, 74, 6280-6288.  
16371706 G.Rosenbaum, R.W.Alkire, G.Evans, F.J.Rotella, K.Lazarski, R.G.Zhang, S.L.Ginell, N.Duke, I.Naday, J.Lazarz, M.J.Molitsky, L.Keefe, J.Gonczy, L.Rock, R.Sanishvili, M.A.Walsh, E.Westbrook, and A.Joachimiak (2006).
The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.
  J Synchrotron Radiat, 13, 30-45.  
16612795 H.Askari, J.Edqvist, M.Hajheidari, M.Kafi, and G.H.Salekdeh (2006).
Effects of salinity levels on proteome of Suaeda aegyptiaca leaves.
  Proteomics, 6, 2542-2554.  
16233902 B.Nocek, C.Chang, H.Li, L.Lezondra, D.Holzle, F.Collart, and A.Joachimiak (2005).
Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes.
  J Mol Biol, 354, 91.
PDB codes: 1yqg 2ag8 2ahr 2amf
16239729 E.W.McKee, L.D.Kanbi, K.L.Childs, R.W.Grosse-Kunstleve, P.D.Adams, J.C.Sacchettini, and T.R.Ioerger (2005).
FINDMOL: automated identification of macromolecules in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 61, 1514-1520.  
16301796 P.Skubák, S.Ness, and N.S.Pannu (2005).
Extending the resolution and phase-quality limits in automated model building with iterative refinement.
  Acta Crystallogr D Biol Crystallogr, 61, 1626-1635.  
15932938 Q.Yang, X.Wang, L.Ye, M.Mentrikoski, E.Mohammadi, Y.M.Kim, and P.C.Maloney (2005).
Experimental tests of a homology model for OxlT, the oxalate transporter of Oxalobacter formigenes.
  Proc Natl Acad Sci U S A, 102, 8513-8518.
PDB code: 1zc7
15333954 M.C.Burla, B.Carrozzini, G.L.Cascarano, C.Giacovazzo, M.Moustiakimov, G.Polidori, and D.Siliqi (2004).
MAD phasing: choosing the most informative wavelength combination.
  Acta Crystallogr D Biol Crystallogr, 60, 1683-1686.  
12657785 M.C.Burla, B.Carrozzini, G.L.Cascarano, C.Giacovazzo, and G.Polidori (2003).
SAD or MAD phasing: location of the anomalous scatterers.
  Acta Crystallogr D Biol Crystallogr, 59, 662-669.  
11807245 C.Alvarez-Rúa, J.Borge, and S.García-Granda (2002).
Combining image-seeking functions and a subtraction strategy: a vector-space procedure to improve many-body searches in molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 58, 215-224.  
12037294 M.C.Burla, B.Carrozzini, G.L.Cascarano, C.Giacovazzo, G.Polidori, and D.Siliqi (2002).
MAD phasing: probabilistic estimate of [F (oa)].
  Acta Crystallogr D Biol Crystallogr, 58, 928-935.  
12351820 T.R.Schneider, and G.M.Sheldrick (2002).
Substructure solution with SHELXD.
  Acta Crystallogr D Biol Crystallogr, 58, 1772-1779.  
11567150 R.W.Grosse-Kunstleve, and P.D.Adams (2001).
Patterson correlation methods: a review of molecular replacement with CNS.
  Acta Crystallogr D Biol Crystallogr, 57, 1390-1396.  
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.