PDBsum entry 1ak0

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Endonuclease PDB id
Protein chain
264 a.a. *
NAG ×2
_ZN ×4
Waters ×154
* Residue conservation analysis
PDB id:
Name: Endonuclease
Title: P1 nuclease in complex with a substrate analog
Structure: P1 nuclease. Chain: a. Ec:
Source: Penicillium citrinum. Organism_taxid: 5077
1.80Å     R-factor:   0.207     R-free:   0.235
Authors: C.Romier,D.Suck
Key ref: C.Romier et al. (1998). Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs. Proteins, 32, 414-424. PubMed id: 9726413
28-May-97     Release date:   03-Dec-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P24289  (NUP1_PENCI) -  Nuclease P1
270 a.a.
264 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Aspergillus nuclease S(1).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products.
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     nucleic acid phosphodiester bond hydrolysis   2 terms 
  Biochemical function     nucleic acid binding     6 terms  


Proteins 32:414-424 (1998)
PubMed id: 9726413  
Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs.
C.Romier, R.Dominguez, A.Lahm, O.Dahl, D.Suck.
The reaction mechanism of nuclease P1 from Penicillium citrinum has been investigated using single-stranded dithiophosphorylated di-, tetra-, and hexanucleotides as substrate analogs. The complexes crystallize in tetragonal and orthorhombic space groups and have been solved by molecular replacement. The high resolution structures give a clear picture of base recognition by P1 nuclease at its two nucleotide-binding sites, especially the 1.8 A structure of a P1-tetranucleotide complex which can be considered a P1-product complex. The observed binding modes are in agreement with a catalytic mechanism where the two closely spaced zinc ions activate the attacking water while the third, more exposed zinc ion stabilizes the leaving 03' oxyanion. Stacking as well as hydrogen bonding interactions with the base 5' to the cleaved phosphodiester bond are important elements of substrate binding and recognition. Modelling of a productive P1-substrate complex based on the solved structures suggests steric hindrance as the likely reason for the resistance of Rp-phosphorothioates and phosphorodithioates. Differences with the highly homologous nuclease S1 from Aspergillus oryzae are discussed.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22785315 T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, and W.Yang (2012).
Watching DNA polymerase η make a phosphodiester bond.
  Nature, 487, 196-201.
PDB codes: 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8
19245837 G.Wang, J.Zhao, and K.M.Vasquez (2009).
Methods to determine DNA structural alterations and genetic instability.
  Methods, 48, 54-62.  
19820715 Y.G.Chen, W.E.Kowtoniuk, I.Agarwal, Y.Shen, and D.R.Liu (2009).
LC/MS analysis of cellular RNA reveals NAD-linked RNA.
  Nat Chem Biol, 5, 879-881.  
18680367 D.G.Su, J.L.Kao, M.L.Gross, and J.S.Taylor (2008).
Structure determination of an interstrand-type cis-anti cyclobutane thymine dimer produced in high yield by UVB light in an oligodeoxynucleotide at acidic pH.
  J Am Chem Soc, 130, 11328-11337.  
17543120 M.Pimkin, E.Caretti, A.Canutescu, J.B.Yeung, H.Cohn, Y.Chen, C.Oleykowski, A.Bellacosa, and A.T.Yeung (2007).
Recombinant nucleases CEL I from celery and SP I from spinach for mutation detection.
  BMC Biotechnol, 7, 29.  
18022364 M.Spies, I.Amitani, R.J.Baskin, and S.C.Kowalczykowski (2007).
RecBCD enzyme switches lead motor subunits in response to chi recognition.
  Cell, 131, 694-705.  
17369272 M.Y.Niv, D.R.Ripoll, J.A.Vila, A.Liwo, E.S.Vanamee, A.K.Aggarwal, H.Weinstein, and H.A.Scheraga (2007).
Topology of Type II REases revisited; structural classes and the common conserved core.
  Nucleic Acids Res, 35, 2227-2237.  
12661000 A.Teplyakov, G.Obmolova, P.P.Khil, A.J.Howard, R.D.Camerini-Otero, and G.L.Gilliland (2003).
Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site.
  Proteins, 51, 315-318.
PDB codes: 1m65 1m68
12441392 M.J.Sui, L.C.Tsai, K.C.Hsia, L.G.Doudeva, W.Y.Ku, G.W.Han, and H.S.Yuan (2002).
Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions.
  Protein Sci, 11, 2947-2957.
PDB code: 1mz8
12403820 S.I.Chamberlin, E.J.Merino, and K.M.Weeks (2002).
Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups.
  Proc Natl Acad Sci U S A, 99, 14688-14693.  
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.