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PDBsum entry 1ogh

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protein links
Hydrolase PDB id
1ogh
Jmol
Contents
Protein chains
175 a.a. *
Waters ×398
* Residue conservation analysis
PDB id:
1ogh
Name: Hydrolase
Title: Structure of the bifunctional dctp deaminase-dutpase from methanocaldococcus jannaschii
Structure: Bifunctional deaminase/diphosphatase. Chain: a, b. Synonym: mjdcd-dut, dcd/dut, (includes\: deoxycytidine triphosphate deaminase, (dctp deaminase), deoxyuridine 5'-triphosphate nucleotidohydrolase, (dutpase, dutp pyrophosphatase)). Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Atcc: 43067. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Trimer (from PDB file)
Resolution:
1.88Å     R-factor:   0.148     R-free:   0.184
Authors: E.Johansson,O.Bjornberg,P.O.Nyman,S.Larsen
Key ref:
E.Johansson et al. (2003). Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii and its relation to other homotrimeric dUTPases. J Biol Chem, 278, 27916-27922. PubMed id: 12756253 DOI: 10.1074/jbc.M304361200
Date:
02-May-03     Release date:   05-Jun-03    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q57872  (DCD_METJA) -  dCTP deaminase, dUMP-forming
Seq:
Struc:
204 a.a.
175 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.4.30  - dCTP deaminase (dUMP-forming).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: dCTP + 2 H2O = dUMP + diphosphate + NH3
dCTP
+ 2 × H(2)O
= dUMP
+ diphosphate
+ NH(3)
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleotide metabolic process   5 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M304361200 J Biol Chem 278:27916-27922 (2003)
PubMed id: 12756253  
 
 
Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii and its relation to other homotrimeric dUTPases.
E.Johansson, O.Bjornberg, P.O.Nyman, S.Larsen.
 
  ABSTRACT  
 
The bifunctional dCTP deaminase-dUTPase (DCD-DUT) from Methanocaldococcus jannaschii catalyzes the deamination of the cytosine moiety in dCTP and the hydrolysis of the triphosphate moiety forming dUMP, thereby preventing uracil from being incorporated into DNA. The crystal structure of DCD-DUT has been determined to 1.88-A resolution and represents the first known structure of an enzyme catalyzing dCTP deamination. The functional form of DCD-DUT is a homotrimer wherein the subunits are composed of a central distorted beta-barrel surrounded by two beta-sheets and four helices. The trimeric DCD-DUT shows structural similarity to trimeric dUTPases at the tertiary and quaternary levels. There are also additional structural elements in DCD-DUT compared with dUTPase because of a longer primary structure. Four of the five conserved sequence motifs that create the active sites in dUTPase are found in structurally equivalent positions in DCD-DUT. The last 25 C-terminal residues of the 204-residue-long DCD-DUT are not visible in the electron density map, but, analogous to dUTPases, the C terminus is probably ordered, closing the active site upon catalysis. Unlike other enzymes catalyzing the deamination of cytosine compounds, DCD-DUT is not exploiting an enzyme-bound metal ion such as zinc or iron for nucleophile generation. The active site contains two water molecules that are engaged in hydrogen bonds to the invariant residues Ser118, Arg122, Thr130, and Glu145. These water molecules are potential nucleophile candidates in the deamination reaction.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Ribbon views of the subunit (a) and the homotrimer (b) of DCD-DUT from M. jannaschii. The -sheets of the subunit are displayed in different shades of blue. The three subunits of the trimer are shown in red, blue, and gray, respectively. c, topology diagram of the dCTP deaminase subunit with the colors of the -sheets corresponding to those in panel a. d, ribbon view of the feline immunodeficiency virus dUTPase homotrimer (PDB code 1F7R [PDB] ) that corresponds to the view in panel b. dUDP is shown in ball-and-stick representation. e, stereo view of M. jannaschii DCD-DUT active site with dUDP and strontium from the equine infectious anemia virus dUTPase complex structure (PDB code 1DUC [PDB] ) superimposed. Residues from the different subunits of the trimer are shown in yellow and orange, respectively. f, stereo view of the hydrogen bonding network, shown with broken lines, in the region of the active site in DCD-DUT where the deamination reaction is assumed to take place. Panels a, b, d, e, and f were prepared with MOLSCRIPT (36) and Raster3D (37).
Figure 3.
FIG. 3. Similarities of DCD-DUT and dUTPase. a, stereo view of the C trace of the superimposed subunits of DCD-DUT from M. jannaschii (magenta) and dUTPase from feline immunodeficiency virus (PDB code 1F7R [PDB] ) (yellow), respectively. Topology diagrams of DCD-DUT (b) and dUTPase (c) from the feline immunodeficiency virus are shown. The equivalent structural elements are displayed in light gray, and the others are shown in dark gray. Panel a was prepared with MOLSCRIPT (36) and Raster3D (37).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 27916-27922) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18837522 B.G.Vértessy, and J.Tóth (2009).
Keeping uracil out of DNA: physiological role, structure and catalytic mechanism of dUTPases.
  Acc Chem Res, 42, 97.  
19251902 H.C.Lee, J.H.Kim, J.S.Kim, W.Jang, and S.Y.Kim (2009).
Fermentative production of thymidine by a metabolically engineered Escherichia coli strain.
  Appl Environ Microbiol, 75, 2423-2432.  
17651436 E.Johansson, M.Thymark, J.H.Bynck, M.Fanø, S.Larsen, and M.Willemoës (2007).
Regulation of dCTP deaminase from Escherichia coli by nonallosteric dTTP binding to an inactive form of the enzyme.
  FEBS J, 274, 4188-4198.
PDB codes: 2j4h 2j4q
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.