PDBsum entry 2par

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
175 a.a. *
TMP ×2
_CO ×2
Waters ×42
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the 5'-deoxynucleotidase yfbr mutant e7 complexed with co(2+) and tmp
Structure: 5'-deoxynucleotidase yfbr. Chain: a, b. Synonym: nucleoside 5'-monophosphate phosphohydrolase, 5'- deoxyribonucleotidase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: yfbr, b2291, jw2288. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.10Å     R-factor:   0.196     R-free:   0.247
Authors: M.D.Zimmerman,M.Proudfoot,A.Yakunin,W.Minor
Key ref:
M.D.Zimmerman et al. (2008). Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli. J Mol Biol, 378, 215-226. PubMed id: 18353368 DOI: 10.1016/j.jmb.2008.02.036
27-Mar-07     Release date:   04-Mar-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P76491  (YFBR_ECOLI) -  5'-deoxynucleotidase YfbR
199 a.a.
175 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - 5'-deoxynucleotidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A 2'-deoxyribonucleoside 5'-monophosphate + H2O = a 2'-deoxyribonucleoside + phosphate
2'-deoxyribonucleoside 5'-monophosphate
Bound ligand (Het Group name = TMP)
matches with 52.17% similarity
+ H(2)O
= 2'-deoxyribonucleoside
Bound ligand (Het Group name = PEG)
matches with 70.00% similarity
+ phosphate
      Cofactor: Cobalt
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     dephosphorylation   3 terms 
  Biochemical function     catalytic activity     9 terms  


    Key reference    
DOI no: 10.1016/j.jmb.2008.02.036 J Mol Biol 378:215-226 (2008)
PubMed id: 18353368  
Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
M.D.Zimmerman, M.Proudfoot, A.Yakunin, W.Minor.
HD-domain phosphohydrolases have nucleotidase and phosphodiesterase activities and play important roles in the metabolism of nucleotides and in signaling. We present three 2.1-A-resolution crystal structures (one in the free state and two complexed with natural substrates) of an HD-domain phosphohydrolase, the Escherichia coli 5'-nucleotidase YfbR. The free-state structure of YfbR contains a large cavity accommodating the metal-coordinating HD motif (H33, H68, D69, and D137) and other conserved residues (R18, E72, and D77). Alanine scanning mutagenesis confirms that these residues are important for activity. Two structures of the catalytically inactive mutant E72A complexed with Co(2+) and either thymidine-5'-monophosphate or 2'-deoxyriboadenosine-5'-monophosphate disclose the novel binding mode of deoxyribonucleotides in the active site. Residue R18 stabilizes the phosphate on the Co(2+), and residue D77 forms a strong hydrogen bond critical for binding the ribose. The indole side chain of W19 is located close to the 2'-carbon atom of the deoxyribose moiety and is proposed to act as the selectivity switch for deoxyribonucleotide, which is supported by comparison to YfdR, another 5'-nucleotidase in E. coli. The nucleotide bases of both deoxyriboadenosine-5'-monophosphate and thymidine-5'-monophosphate make no specific hydrogen bonds with the protein, explaining the lack of nucleotide base selectivity. The YfbR E72A substrate complex structures also suggest a plausible single-step nucleophilic substitution mechanism. This is the first proposed molecular mechanism for an HD-domain phosphohydrolase based directly on substrate-bound crystal structures.
  Selected figure(s)  
Figure 5.
Fig. 5. Schematic representation of the binding mode of TMP to YfbR E72A. Protein residues are shown with brown bonds, TMP is shown with purple bonds, and Co^2+ is shown as a green sphere. Atoms and residues involved in van der Waals contacts are marked with red lines. Substrate–protein hydrogen bonds and cation contacts are shown as green lines, with bond distances in angstroms.
Figure 7.
Fig. 7. Proposed mechanism for catalytic activity of YfbR. (a) Stereo view of the binding site of YfbR E72A (light gray) superimposed on WT YfbR (yellow). Waters from YfbR E72A and from wild-type YfbR are shown as gray and yellow spheres, respectively. (b) Schematic of a possible catalytic mechanism.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 378, 215-226) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21613998 N.Laguette, B.Sobhian, N.Casartelli, M.Ringeard, C.Chable-Bessia, E.Ségéral, A.Yatim, S.Emiliani, O.Schwartz, and M.Benkirane (2011).
SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx.
  Nature, 474, 654-657.  
20818390 D.Sun, G.Lee, J.H.Lee, H.Y.Kim, H.W.Rhee, S.Y.Park, K.J.Kim, Y.Kim, B.Y.Kim, J.I.Hong, C.Park, H.E.Choy, J.H.Kim, Y.H.Jeon, and J.Chung (2010).
A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses.
  Nat Struct Mol Biol, 17, 1188-1194.
PDB codes: 3nqw 3nr1
20363937 Y.Zhang, E.L.Pohlmann, J.Serate, M.C.Conrad, and G.P.Roberts (2010).
Mutagenesis and functional characterization of the four domains of GlnD, a bifunctional nitrogen sensor protein.
  J Bacteriol, 192, 2711-2721.  
19525956 G.I.Rice, J.Bond, A.Asipu, R.L.Brunette, I.W.Manfield, I.M.Carr, J.C.Fuller, R.M.Jackson, T.Lamb, T.A.Briggs, M.Ali, H.Gornall, L.R.Couthard, A.Aeby, S.P.Attard-Montalto, E.Bertini, C.Bodemer, K.Brockmann, L.A.Brueton, P.C.Corry, I.Desguerre, E.Fazzi, A.G.Cazorla, B.Gener, B.C.Hamel, A.Heiberg, M.Hunter, M.S.van der Knaap, R.Kumar, L.Lagae, P.G.Landrieu, C.M.Lourenco, D.Marom, M.F.McDermott, W.van der Merwe, S.Orcesi, J.S.Prendiville, M.Rasmussen, S.A.Shalev, D.M.Soler, M.Shinawi, R.Spiegel, T.Y.Tan, A.Vanderver, E.L.Wakeling, E.Wassmer, E.Whittaker, P.Lebon, D.B.Stetson, D.T.Bonthron, and Y.J.Crow (2009).
Mutations involved in Aicardi-Goutières syndrome implicate SAMHD1 as regulator of the innate immune response.
  Nat Genet, 41, 829-832.  
19808788 Y.J.Crow, and J.Rehwinkel (2009).
Aicardi-Goutieres syndrome and related phenotypes: linking nucleic acid metabolism with autoimmunity.
  Hum Mol Genet, 18, R130-R136.  
18844997 H.T.Tran, J.Krushkal, F.M.Antommattei, D.R.Lovley, and R.M.Weis (2008).
Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function.
  BMC Genomics, 9, 471.  
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.