PDBsum entry 1qsl

Go to PDB code: 
protein dna_rna metals links
Transferase/DNA PDB id
Protein chain
601 a.a. *
Waters ×191
* Residue conservation analysis
PDB id:
Name: Transferase/DNA
Title: Klenow fragment complexed with single-stranded substrate and (iii) ion
Structure: 5'-d( Gp Cp Tp Tp Ap Cp Gp C)-3'. Chain: b. Engineered: yes. DNA polymerase i. Chain: a. Fragment: klenow fragment. Synonym: pol i. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Other_details: chemically synthesized by standard phosphora methodology. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.20Å     R-factor:   0.214     R-free:   0.255
Authors: C.A.Brautigam,K.Aschheim,T.A.Steitz
Key ref: C.A.Brautigam et al. (1999). Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment. Chem Biol, 6, 901-908. PubMed id: 10631518
22-Jun-99     Release date:   30-Jun-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00582  (DPO1_ECOLI) -  DNA polymerase I
928 a.a.
601 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.  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleobase-containing compound metabolic process   3 terms 
  Biochemical function     nucleic acid binding     4 terms  


Chem Biol 6:901-908 (1999)
PubMed id: 10631518  
Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment.
C.A.Brautigam, K.Aschheim, T.A.Steitz.
BACKGROUND: Biochemical and biophysical experiments have shown that two catalytically essential divalent metal ions (termed 'A' and 'B') bind to the 3'-5' exonuclease active site of the Klenow fragment (KF) of Escherichia coli DNA polymerase I. X-ray crystallographic studies have established the normal positions in the KF 3'-5' exonuclease (KF exo) active site of the two cations and the single-stranded DNA substrate. Lanthanide (III) luminescence studies have demonstrated, however, that only a single europium (III) ion (Eu3+) binds to the KF exo active site. Furthermore, Eu3+ does not support catalysis by KF exo or several other two-metal-ion phosphoryl-transfer enzymes. RESULTS: A crystal structure of KF complexed with both Eu3+ and substrate single-stranded oligodeoxynucleotide shows that a lone Eu3+ is bound near to metal-ion site A. Comparison of this structure to a relevant native structure reveals that the bound Eu3+ causes a number of changes to the KF exo active site. The scissile phosphate of the substrate is displaced from its normal position by about 1 A when Eu3+ is bound and the presence of Eu3+ in the active site precludes the binding of the essential metal ion B. CONCLUSIONS: The substantial, lanthanide-induced differences in metal-ion and substrate binding to KF exo account for the inhibition of this enzyme by Eu3+. These changes also explain the inability of KF exo to bind more than one cation in the presence of lanthanides. The mechanistic similarity between KF exo and other two-metal-ion phosphoryl-transfer enzymes suggests that the principles of lanthanide (III) ion binding and inhibition ascertained from this study will probably apply to most members of this class of enzymes.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21425348 L.Martínez, T.E.Malliavin, and A.Blondel (2011).
Mechanism of reactant and product dissociation from the anthrax edema factor: A locally enhanced sampling and steered molecular dynamics study.
  Proteins, 79, 1649-1661.  
19529883 X.C.Su, and G.Otting (2010).
Paramagnetic labelling of proteins and oligonucleotides for NMR.
  J Biomol NMR, 46, 101-112.  
18780819 M.Brucet, J.Querol-Audí, K.Bertlik, J.Lloberas, I.Fita, and A.Celada (2008).
Structural and biochemical studies of TREX1 inhibition by metals. Identification of a new active histidine conserved in DEDDh exonucleases.
  Protein Sci, 17, 2059-2069.
PDB codes: 3b6o 3b6p
17311351 D.Chen, G.Menche, T.D.Power, L.Sower, J.W.Peterson, and C.H.Schein (2007).
Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins.
  Proteins, 67, 593-605.  
16767502 C.Schmitz, M.John, A.Y.Park, N.E.Dixon, G.Otting, G.Pintacuda, and T.Huber (2006).
Efficient chi-tensor determination and NH assignment of paramagnetic proteins.
  J Biomol NMR, 35, 79-87.  
16622405 J.J.Perry, S.M.Yannone, L.G.Holden, C.Hitomi, A.Asaithamby, S.Han, P.K.Cooper, D.J.Chen, and J.A.Tainer (2006).
WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing.
  Nat Struct Mol Biol, 13, 414-422.
PDB codes: 2fbt 2fbv 2fbx 2fby 2fc0
15719022 Y.Shen, N.L.Zhukovskaya, Q.Guo, J.Florián, and W.J.Tang (2005).
Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor.
  EMBO J, 24, 929-941.
PDB codes: 1xfu 1xfv 1xfw 1xfx 1xfy 1xfz 1y0v
15131111 Q.Guo, Y.Shen, N.L.Zhukovskaya, J.Florián, and W.J.Tang (2004).
Structural and kinetic analyses of the interaction of anthrax adenylyl cyclase toxin with reaction products cAMP and pyrophosphate.
  J Biol Chem, 279, 29427-29435.
PDB code: 1sk6
15358788 Y.G.Ren, L.A.Kirsebom, and A.Virtanen (2004).
Coordination of divalent metal ions in the active site of poly(A)-specific ribonuclease.
  J Biol Chem, 279, 48702-48706.  
14580211 L.M.Bowen, and C.M.Dupureur (2003).
Investigation of restriction enzyme cofactor requirements: a relationship between metal ion properties and sequence specificity.
  Biochemistry, 42, 12643-12653.  
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.