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| Enzyme Name | | Swiss-prot | KEGG |
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| P03697 |
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| Protein name | Exonuclease | exodeoxyribonuclease (lambda-induced)lambda exonucleasephage lambda-induced exonucleaseEscherichia coli exonuclease IVE. coli exonuclease IVexodeoxyribonuclease IVexonuclease IV |
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| Synonyms | EC 3.1.11.3 |
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| Swiss-prot:Accession Number | P03697 |
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| Entry name | EXO_LAMBD |
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| Activity | Exonucleolytic cleavage in the 5''- to 3''- direction to yield nucleoside 5''-phosphates. |
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| Subunit | Trimer of three subunits that form a toroid, with a tapered channel passing through the middle. |
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| Subcellular location |
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| Cofactor | Magnesium. |
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| Cofactors | Substrates | Products |
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| KEGG-id | C00305 | C00039 | C00001 | C01150 |
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| Compound | magnesium | DNA | H2O | 5'-Phosphomononucleotides |
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| Type | divalent metal (Ca2+, Mg2+) | nucleic acids | H2O | nucleotide |
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| 1avqA |  | Unbound | Unbound |
| Unbound |
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| 1avqB | | Unbound | Unbound |
| Unbound |
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| 1avqC | | Unbound | Unbound |
| Unbound |
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| Active-site residues | | resource |
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| literature [4] | | pdb | Catalytic residues | Cofactor-binding residues |
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| 1avqA | | LYS 131
| ASP 119;GLU 129 (Mg2+ binding)
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| 1avqB | | LYS 131
| ASP 119;GLU 129 (Mg2+ binding)
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| 1avqC | | LYS 131
| ASP 119;GLU 129 (Mg2+ binding)
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| References for Catalytic Mechanism | | References | Sections | No. of steps in catalysis |
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| [2] | Fig.8, Fig.11, p.12-17 | 2 | | [3] | Fig.5, p.13492-13494 | 2 | | [4] | p.7895-7896 |
| | [5] | Fig.1, p.6 |
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| references | | [1] |
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| Comments | X-ray crystallography (2.4 Angstroms) |
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| PubMed ID | 9295273 |
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| Journal | Science |
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| Year | 1997 |
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| Volume | 277 |
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| Pages | 1824-7 |
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| Authors | Kovall R, Matthews BW |
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| Title | Toroidal structure of lambda-exonuclease. |
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| Related PDB | 1avq |
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| [2] |
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| Comments | catalysis |
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| PubMed ID | 9210460 |
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| Journal | Eur J Biochem |
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| Year | 1997 |
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| Volume | 246 |
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| Pages | 1-22 |
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| Authors | Pingoud A, Jeltsch A |
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| Title | Recognition and cleavage of DNA by type-II restriction endonucleases. |
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| [3] |
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| Comments | X-ray crystallography (2.15 Angstroms) |
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| PubMed ID | 9811827 |
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| Journal | Proc Natl Acad Sci U S A |
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| Year | 1998 |
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| Volume | 95 |
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| Pages | 13489-94 |
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| Authors | Horton NC, Newberry KJ, Perona JJ |
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| Title | Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. |
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| [4] |
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| Comments | Structural, functional, and evolutionary relationships of the other enzyme |
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| PubMed ID | 9653111 |
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| Journal | Proc Natl Acad Sci U S A |
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| Year | 1998 |
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| Volume | 95 |
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| Pages | 7893-7 |
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| Authors | Kovall RA, Matthews BW |
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| Title | Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases. |
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| [5] |
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| PubMed ID | 10739241 |
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| Journal | Protein Sci |
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| Year | 2000 |
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| Volume | 9 |
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| Pages | 1-9 |
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| Authors | Dall'Acqua W, Carter P |
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| Title | Substrate-assisted catalysis: molecular basis and biological significance. |
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| comments | According to the literature [4], the active site of this enzyme is very similar to those of type II endonucleases, such as EcoRV and PvuII. Thus, the paper suggested that the catalytic mechanism can be similar to those of enzymes [4] (see [2] & [3]).
More recent paper [5] supported the substrate-assisted mechanism for the related enzymes (type II restriction enzymes), ruling out the two-metal-ion mechanism. Thus, we concluded that this enzyme adopts the substrate-assisted mechanism with only one metal ion for catalysis (see EcoRV; S00404 in EzCatDB).
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| created | updated |
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| 2002-07-01 | 2009-02-26 |
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