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PDBsum entry 1exn

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protein links
Nuclease PDB id
1exn
Jmol
Contents
Protein chains
271 a.a. *
Waters ×226
* Residue conservation analysis
PDB id:
1exn
Name: Nuclease
Title: T5 5'-exonuclease
Structure: 5'-exonuclease. Chain: a, b. Synonym: 5'-nuclease. 5'-3' exonuclease. Engineered: yes. Mutation: yes
Source: Enterobacteria phage t5. Organism_taxid: 10726. Gene: d15. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.50Å     R-factor:   0.227     R-free:   0.339
Authors: T.A.Ceska,J.R.Sayers,G.Stier,D.Suck
Key ref: T.A.Ceska et al. (1996). A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease. Nature, 382, 90-93. PubMed id: 8657312
Date:
17-Jan-97     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06229  (EXO5_BPT5) -  Exodeoxyribonuclease
Seq:
Struc:
291 a.a.
271 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.11.3  - Exodeoxyribonuclease (lambda-induced).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Degradation of double-stranded DNA. It acts progressively in a 5'- to 3'-direction, releasing nucleoside 5'-phosphates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
Nature 382:90-93 (1996)
PubMed id: 8657312  
 
 
A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.
T.A.Ceska, J.R.Sayers, G.Stier, D.Suck.
 
  ABSTRACT  
 
THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been shown to possess endonucleolytic activities. T5 5'-3'-exonuclease shares many similarities with the amino terminal of eubacterial DNA polymerases, although, unlike eubacteria, phages such as T5, T4 and T7 express polymerase and 5'-exonuclease proteins from separate genes. Here we report the 2.5-A crystal structure of the phage T5 5'-exonuclease, which reveals a helical arch for binding DNA. We propose a model consistent with a threading mechanism in which single-stranded DNA could slide through the arch, which is formed by two helices, one containing positively charged, and the other hydrophobic, residues. The active site is at the base of the arch, and contains two metal-binding sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21496642 J.Orans, E.A.McSweeney, R.R.Iyer, M.A.Hast, H.W.Hellinga, P.Modrich, and L.S.Beese (2011).
Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family.
  Cell, 145, 212-223.
PDB codes: 3qe9 3qea 3qeb
21264264 P.Xie, and J.R.Sayers (2011).
A model for transition of 5'-nuclease domain of DNA polymerase I from inert to active modes.
  PLoS One, 6, e16213.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
19934252 J.A.Stewart, J.L.Campbell, and R.A.Bambara (2010).
Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates.
  Nucleic Acids Res, 38, 920-930.  
19188255 C.Sissi, and M.Palumbo (2009).
Effects of magnesium and related divalent metal ions in topoisomerase structure and function.
  Nucleic Acids Res, 37, 702-711.  
19525235 L.D.Finger, M.S.Blanchard, C.A.Theimer, B.Sengerová, P.Singh, V.Chavez, F.Liu, J.A.Grasby, and B.Shen (2009).
The 3'-flap pocket of human flap endonuclease 1 is critical for substrate binding and catalysis.
  J Biol Chem, 284, 22184-22194.  
19000038 L.M.Allen, M.R.Hodskinson, and J.R.Sayers (2009).
Active site substitutions delineate distinct classes of eubacterial flap endonuclease.
  Biochem J, 418, 285-292.  
18344366 F.Rao, Y.Yang, Y.Qi, and Z.X.Liang (2008).
Catalytic mechanism of cyclic di-GMP-specific phosphodiesterase: a study of the EAL domain-containing RocR from Pseudomonas aeruginosa.
  J Bacteriol, 190, 3622-3631.  
18697748 K.Syson, C.Tomlinson, B.R.Chapados, J.R.Sayers, J.A.Tainer, N.H.Williams, and J.A.Grasby (2008).
Three metal ions participate in the reaction catalyzed by t5 flap endonuclease.
  J Biol Chem, 283, 28741-28746.  
  19181113 O.D.Schärer (2008).
XPG: its products and biological roles.
  Adv Exp Med Biol, 637, 83-92.  
18398909 R.D.Bunker, J.L.McKenzie, E.N.Baker, and V.L.Arcus (2008).
Crystal structure of PAE0151 from Pyrobaculum aerophilum, a PIN-domain (VapC) protein from a toxin-antitoxin operon.
  Proteins, 72, 510-518.
PDB code: 2fe1
  18097100 S.Sakurai, K.Kitano, H.Morioka, and T.Hakoshima (2008).
Crystallization and preliminary crystallographic analysis of the catalytic domain of human flap endonuclease 1 in complex with a nicked DNA product: use of a DPCS kit for efficient protein-DNA complex crystallization.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 39-43.  
17557331 D.Takeshita, S.Zenno, W.C.Lee, K.Saigo, and M.Tanokura (2007).
Crystal structure of the PIN domain of human telomerase-associated protein EST1A.
  Proteins, 68, 980-989.
PDB code: 2dok
17693399 J.M.Devos, S.J.Tomanicek, C.E.Jones, N.G.Nossal, and T.C.Mueser (2007).
Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates.
  J Biol Chem, 282, 31713-31724.
PDB code: 2ihn
17452369 M.Hohl, I.Dunand-Sauthier, L.Staresincic, P.Jaquier-Gubler, F.Thorel, M.Modesti, S.G.Clarkson, and O.D.Schärer (2007).
Domain swapping between FEN-1 and XPG defines regions in XPG that mediate nucleotide excision repair activity and substrate specificity.
  Nucleic Acids Res, 35, 3053-3063.  
17567612 M.R.Hodskinson, L.M.Allen, D.P.Thomson, and J.R.Sayers (2007).
Molecular interactions of Escherichia coli ExoIX and identification of its associated 3'-5' exonuclease activity.
  Nucleic Acids Res, 35, 4094-4102.  
17559871 R.Williams, B.Sengerová, S.Osborne, K.Syson, S.Ault, A.Kilgour, B.R.Chapados, J.A.Tainer, J.R.Sayers, and J.A.Grasby (2007).
Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease.
  J Mol Biol, 371, 34-48.  
15954100 B.Shen, P.Singh, R.Liu, J.Qiu, L.Zheng, L.D.Finger, and S.Alas (2005).
Multiple but dissectible functions of FEN-1 nucleases in nucleic acid processing, genome stability and diseases.
  Bioessays, 27, 717-729.  
15590680 I.Dunand-Sauthier, M.Hohl, F.Thorel, P.Jaquier-Gubler, S.G.Clarkson, and O.D.Schärer (2005).
The spacer region of XPG mediates recruitment to nucleotide excision repair complexes and determines substrate specificity.
  J Biol Chem, 280, 7030-7037.  
15616578 S.Sakurai, K.Kitano, H.Yamaguchi, K.Hamada, K.Okada, K.Fukuda, M.Uchida, E.Ohtsuka, H.Morioka, and T.Hakoshima (2005).
Structural basis for recruitment of human flap endonuclease 1 to PCNA.
  EMBO J, 24, 683-693.
PDB code: 1ul1
15333952 B.K.Collins, S.J.Tomanicek, N.Lyamicheva, M.W.Kaiser, and T.C.Mueser (2004).
A preliminary solubility screen used to improve crystallization trials: crystallization and preliminary X-ray structure determination of Aeropyrum pernix flap endonuclease-1.
  Acta Crystallogr D Biol Crystallogr, 60, 1674-1678.  
15247286 D.L.Ho, W.M.Byrnes, W.P.Ma, Y.Shi, D.J.Callaway, and Z.Bu (2004).
Structure-specific DNA-induced conformational changes in Taq polymerase revealed by small angle neutron scattering.
  J Biol Chem, 279, 39146-39154.  
15131255 E.Friedrich-Heineken, and U.Hübscher (2004).
The Fen1 extrahelical 3'-flap pocket is conserved from archaea to human and regulates DNA substrate specificity.
  Nucleic Acids Res, 32, 2520-2528.  
14742430 E.Matsui, J.Abe, H.Yokoyama, and I.Matsui (2004).
Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.
  J Biol Chem, 279, 16687-16696.  
15448135 H.I.Kao, J.L.Campbell, and R.A.Bambara (2004).
Dna2p helicase/nuclease is a tracking protein, like FEN1, for flap cleavage during Okazaki fragment maturation.
  J Biol Chem, 279, 50840-50849.  
15211526 I.Levin, R.Schwarzenbacher, R.Page, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.Campbell, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, K.Quijano, R.Reyes, F.Rezezadeh, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, and I.A.Wilson (2004).
Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution.
  Proteins, 56, 404-408.
PDB code: 1o4w
15037610 J.Qiu, R.Liu, B.R.Chapados, M.Sherman, J.A.Tainer, and B.Shen (2004).
Interaction interface of human flap endonuclease-1 with its DNA substrates.
  J Biol Chem, 279, 24394-24402.  
15077103 M.Feng, D.Patel, J.J.Dervan, T.Ceska, D.Suck, I.Haq, and J.R.Sayers (2004).
Roles of divalent metal ions in flap endonuclease-substrate interactions.
  Nat Struct Mol Biol, 11, 450-456.
PDB codes: 1ut5 1ut8
14734548 V.L.Arcus, K.Bäckbro, A.Roos, E.L.Daniel, and E.N.Baker (2004).
Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease.
  J Biol Chem, 279, 16471-16478.
PDB codes: 1v8o 1v8p
15189154 Y.Liu, H.I.Kao, and R.A.Bambara (2004).
Flap endonuclease 1: a central component of DNA metabolism.
  Annu Rev Biochem, 73, 589-615.  
15082797 Y.Liu, H.Zhang, J.Veeraraghavan, R.A.Bambara, and C.H.Freudenreich (2004).
Saccharomyces cerevisiae flap endonuclease 1 uses flap equilibration to maintain triplet repeat stability.
  Mol Cell Biol, 24, 4049-4064.  
12606565 M.R.Tock, E.Frary, J.R.Sayers, and J.A.Grasby (2003).
Dynamic evidence for metal ion catalysis in the reaction mediated by a flap endonuclease.
  EMBO J, 22, 995.  
12586391 N.A.Desai, and V.Shankar (2003).
Single-strand-specific nucleases.
  FEMS Microbiol Rev, 26, 457-491.  
11972066 A.Yamagata, Y.Kakuta, R.Masui, and K.Fukuyama (2002).
The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.
  Proc Natl Acad Sci U S A, 99, 5908-5912.
PDB code: 1ir6
11842105 B.I.Lee Bi, L.H.Nguyen, D.Barsky, M.Fernandes, and D.M.Wilson (2002).
Molecular interactions of human Exo1 with DNA.
  Nucleic Acids Res, 30, 942-949.  
12163576 D.N.Everly, P.Feng, I.S.Mian, and G.S.Read (2002).
mRNA degradation by the virion host shutoff (Vhs) protein of herpes simplex virus: genetic and biochemical evidence that Vhs is a nuclease.
  J Virol, 76, 8560-8571.  
12147694 E.Matsui, K.V.Musti, J.Abe, K.Yamasaki, I.Matsui, and K.Harata (2002).
Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1 from Pyrococcus horikoshii.
  J Biol Chem, 277, 37840-37847.
PDB code: 1mc8
12411510 F.Storici, G.Henneke, E.Ferrari, D.A.Gordenin, U.Hübscher, and M.A.Resnick (2002).
The flexible loop of human FEN1 endonuclease is required for flap cleavage during DNA replication and repair.
  EMBO J, 21, 5930-5942.  
11825897 H.I.Kao, L.A.Henricksen, Y.Liu, and R.A.Bambara (2002).
Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate.
  J Biol Chem, 277, 14379-14389.  
12084915 J.J.Dervan, M.Feng, D.Patel, J.A.Grasby, P.J.Artymiuk, T.A.Ceska, and J.R.Sayers (2002).
Interactions of mutant and wild-type flap endonucleases with oligonucleotide substrates suggest an alternative model of DNA binding.
  Proc Natl Acad Sci U S A, 99, 8542-8547.
PDB code: 1j5f
11986308 J.Qiu, D.N.Bimston, A.Partikian, and B.Shen (2002).
Arginine residues 47 and 70 of human flap endonuclease-1 are involved in DNA substrate interactions and cleavage site determination.
  J Biol Chem, 277, 24659-24666.  
12162748 L.Zheng, M.Li, J.Shan, R.Krishnamoorthi, and B.Shen (2002).
Distinct roles of two Mg2+ binding sites in regulation of murine flap endonuclease-1 activities.
  Biochemistry, 41, 10323-10331.  
11433022 S.J.Garforth, D.Patel, M.Feng, and J.R.Sayers (2001).
Unusually wide co-factor tolerance in a metalloenzyme; divalent metal ions modulate endo-exonuclease activity in T5 exonuclease.
  Nucleic Acids Res, 29, 2772-2779.  
11438646 Y.Xie, Y.Liu, J.L.Argueso, L.A.Henricksen, H.I.Kao, R.A.Bambara, and E.Alani (2001).
Identification of rad27 mutations that confer differential defects in mutation avoidance, repeat tract instability, and flap cleavage.
  Mol Cell Biol, 21, 4889-4899.  
10744741 S.Tom, L.A.Henricksen, and R.A.Bambara (2000).
Mechanism whereby proliferating cell nuclear antigen stimulates flap endonuclease 1.
  J Biol Chem, 275, 10498-10505.  
10908318 X.Shao, and N.V.Grishin (2000).
Common fold in helix-hairpin-helix proteins.
  Nucleic Acids Res, 28, 2643-2650.  
10026181 A.Constantinou, D.Gunz, E.Evans, P.Lalle, P.A.Bates, R.D.Wood, and S.G.Clarkson (1999).
Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair.
  J Biol Chem, 274, 5637-5648.  
10329652 J.A.Rumbaugh, L.A.Henricksen, M.S.DeMott, and R.A.Bambara (1999).
Cleavage of substrates with mismatched nucleotides by Flap endonuclease-1. Implications for mammalian Okazaki fragment processing.
  J Biol Chem, 274, 14602-14608.  
  10454540 J.A.Solinger, D.Pascolini, and W.D.Heyer (1999).
Active-site mutations in the Xrn1p exoribonuclease of Saccharomyces cerevisiae reveal a specific role in meiosis.
  Mol Cell Biol, 19, 5930-5942.  
  10567561 J.Qiu, Y.Qian, P.Frank, U.Wintersberger, and B.Shen (1999).
Saccharomyces cerevisiae RNase H(35) functions in RNA primer removal during lagging-strand DNA synthesis, most efficiently in cooperation with Rad27 nuclease.
  Mol Cell Biol, 19, 8361-8371.  
10064579 K.K.Leuther, O.Hammarsten, R.D.Kornberg, and G.Chu (1999).
Structure of DNA-dependent protein kinase: implications for its regulation by DNA.
  EMBO J, 18, 1114-1123.  
10409700 M.W.Kaiser, N.Lyamicheva, W.Ma, C.Miller, B.Neri, L.Fors, and V.I.Lyamichev (1999).
A comparison of eubacterial and archaeal structure-specific 5'-exonucleases.
  J Biol Chem, 274, 21387-21394.  
9874768 S.J.Garforth, T.A.Ceska, D.Suck, and J.R.Sayers (1999).
Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3' exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage.
  Proc Natl Acad Sci U S A, 96, 38-43.
PDB code: 1xo1
10364212 T.J.Pickering, S.Garforth, J.R.Sayers, and J.A.Grasby (1999).
Variation in the steady state kinetic parameters of wild type and mutant T5 5'-3'-exonuclease with pH. Protonation of Lys-83 is critical for DNA binding.
  J Biol Chem, 274, 17711-17717.  
10339555 V.Lyamichev, M.A.Brow, V.E.Varvel, and J.E.Dahlberg (1999).
Comparison of the 5' nuclease activities of taq DNA polymerase and its isolated nuclease domain.
  Proc Natl Acad Sci U S A, 96, 6143-6148.  
9612080 B.Shen, J.Qiu, D.Hosfield, and J.A.Tainer (1998).
Flap endonuclease homologs in archaebacteria exist as independent proteins.
  Trends Biochem Sci, 23, 171-173.  
9822618 C.Schulze, A.Jeltsch, I.Franke, C.Urbanke, and A.Pingoud (1998).
Crosslinking the EcoRV restriction endonuclease across the DNA-binding site reveals transient intermediates and conformational changes of the enzyme during DNA binding and catalytic turnover.
  EMBO J, 17, 6757-6766.  
9778254 D.J.Hosfield, C.D.Mol, B.Shen, and J.A.Tainer (1998).
Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity.
  Cell, 95, 135-146.
PDB code: 1b43
9765234 D.J.Hosfield, G.Frank, Y.Weng, J.A.Tainer, and B.Shen (1998).
Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1.
  J Biol Chem, 273, 27154-27161.  
9685493 D.M.Wilson, J.P.Carney, M.A.Coleman, A.W.Adamson, M.Christensen, and J.E.Lamerdin (1998).
Hex1: a new human Rad2 nuclease family member with homology to yeast exonuclease 1.
  Nucleic Acids Res, 26, 3762-3768.  
9830061 G.Frank, J.Qiu, M.Somsouk, Y.Weng, L.Somsouk, J.P.Nolan, and B.Shen (1998).
Partial functional deficiency of E160D flap endonuclease-1 mutant in vitro and in vivo is due to defective cleavage of DNA substrates.
  J Biol Chem, 273, 33064-33072.  
  9765572 H.G.Rao, A.Rosenfeld, and J.G.Wetmur (1998).
Methanococcus jannaschii flap endonuclease: expression, purification, and substrate requirements.
  J Bacteriol, 180, 5406-5412.  
9699623 J.R.Sayers, and P.J.Artymiuk (1998).
Flexible loops and helical arches.
  Nat Struct Biol, 5, 668-670.  
9699635 K.Y.Hwang, K.Baek, H.Y.Kim, and Y.Cho (1998).
The crystal structure of flap endonuclease-1 from Methanococcus jannaschii.
  Nat Struct Biol, 5, 707-713.
PDB codes: 1a76 1a77
9476890 T.A.Baker, and S.P.Bell (1998).
Polymerases and the replisome: machines within machines.
  Cell, 92, 295-305.  
9808040 Y.C.Yuan, R.H.Whitson, Q.Liu, K.Itakura, and Y.Chen (1998).
A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
  Nat Struct Biol, 5, 959-964.
PDB code: 1bmy
9241249 B.Shen, J.P.Nolan, L.A.Sklar, and M.S.Park (1997).
Functional analysis of point mutations in human flap endonuclease-1 active site.
  Nucleic Acids Res, 25, 3332-3338.  
9171819 D.A.Gordenin, T.A.Kunkel, and M.A.Resnick (1997).
Repeat expansion--all in a flap?
  Nat Genet, 16, 116-118.  
9782777 D.Suck (1997).
DNA recognition by structure-selective nucleases.
  Biopolymers, 44, 405-421.  
9353315 M.Bhagwat, D.Meara, and N.G.Nossal (1997).
Identification of residues of T4 RNase H required for catalysis and DNA binding.
  J Biol Chem, 272, 28531-28538.  
9353314 M.Bhagwat, L.J.Hobbs, and N.G.Nossal (1997).
The 5'-exonuclease activity of bacteriophage T4 RNase H is stimulated by the T4 gene 32 single-stranded DNA-binding protein, but its flap endonuclease is inhibited.
  J Biol Chem, 272, 28523-28530.  
9312036 M.G.Kramer, S.A.Khan, and M.Espinosa (1997).
Plasmid rolling circle replication: identification of the RNA polymerase-directed primer RNA and requirement for DNA polymerase I for lagging strand synthesis.
  EMBO J, 16, 5784-5795.  
9080773 M.R.Lieber (1997).
The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair.
  Bioessays, 19, 233-240.  
9336450 P.J.Artymiuk, T.A.Ceska, D.Suck, and J.R.Sayers (1997).
Prokaryotic 5'-3' exonucleases share a common core structure with gamma-delta resolvase.
  Nucleic Acids Res, 25, 4224-4229.  
9295277 R.D.Wood (1997).
Nucleotide excision repair in mammalian cells.
  J Biol Chem, 272, 23465-23468.  
9380501 S.J.Garforth, and J.R.Sayers (1997).
Structure-specific DNA binding by bacteriophage T5 5'-->3' exonuclease.
  Nucleic Acids Res, 25, 3801-3807.  
9115419 T.Lindahl, P.Karran, and R.D.Wood (1997).
DNA excision repair pathways.
  Curr Opin Genet Dev, 7, 158-169.  
8987401 P.N.Hengen (1996).
Methods and reagents. Eliminating ghost bands from plasmid preps.
  Trends Biochem Sci, 21, 441-442.  
9016652 V.Mizrahi, and P.Huberts (1996).
Deoxy- and dideoxynucleotide discrimination and identification of critical 5' nuclease domain residues of the DNA polymerase I from Mycobacterium tuberculosis.
  Nucleic Acids Res, 24, 4845-4852.  
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.