DB code: T00228
| CATH domain | 3.30.66.10 : Viral Topoisomerase I | |
|---|---|---|
| 3.90.15.10 : Topoisomerase I; Chain A, domain 3 | ||
| 1.20.120.380 : Four Helix Bundle (Hemerythrin (Met), subunit A) | Catalytic domain | |
| E.C. | 5.99.1.2 | |
| CSA | ||
| M-CSA | ||
| MACiE | M0232 | |
| CATH domain | Related DB codes (homologues) |
|---|---|
| 3.90.15.10 : Topoisomerase I; Chain A, domain 3 | M00047 M00182 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | Pfam |
|---|---|---|---|---|
| P68698 |
DNA topoisomerase 1
|
EC
5.99.1.2
DNA topoisomerase I Late protein H7 |
YP_232986.1
(Protein)
NC_006998.1 (DNA/RNA sequence) |
PF01028
(Topoisom_I)
PF09266 (VirDNA-topo-I_N) [Graphical View] |
| KEGG enzyme name |
|---|
|
DNA topoisomerase
type I DNA topoisomerase untwisting enzyme relaxing enzyme nicking-closing enzyme swivelase omega-protein deoxyribonucleate topoisomerase topoisomerase type I DNA topoisomerase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P68698 | TOP1_VACCV | ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. |
| KEGG Pathways | Map code | Pathways | E.C. |
|---|
| Compound table | ||||||||
|---|---|---|---|---|---|---|---|---|
| Substrates | Products | Intermediates | ||||||
| KEGG-id | C00271 | C00271 | ||||||
| E.C. | ||||||||
| Compound | Single-stranded DNA | Single-stranded DNA | ||||||
| Type | nucleic acids | nucleic acids | ||||||
| ChEBI | ||||||||
| PubChem | ||||||||
| 1vccA |
|
|
|
|
|
Unbound | Unbound | |
| 1a41A01 |
|
|
|
|
|
Unbound | Unbound | |
| 1a41A02 |
|
|
|
|
|
Unbound | Unbound | |
| Reference for Active-site residues | ||
|---|---|---|
| resource | references | E.C. |
| Swiss-prot;P08585 | ||
| Active-site residues | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PDB | Catalytic residues | Cofactor-binding residues | Modified residues | Main-chain involved in catalysis | Comment | |||||
| 1vccA |
|
|
|
|
|
|||||
| 1a41A01 |
|
|
|
|
|
|||||
| 1a41A02 |
|
|
|
|
|
TYR 274 | ||||
| References for Catalytic Mechanism | ||
|---|---|---|
| References | Sections | No. of steps in catalysis |
|
[3]
|
p.8626-8627 | |
|
[4]
|
Fig.6A, p.15456-15457 | |
|
[8]
|
||
|
[10]
|
p.3007-3008 | |
|
[11]
|
Fig.2, p.322-335 | |
|
[12]
|
p.845-846 | |
|
[14]
|
Fig.10 | |
|
[15]
|
p.33 | |
|
[16]
|
Fig.1 | |
|
[17]
|
p.3327 | |
|
[19]
|
||
| References | |
|---|---|
| [1] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 2852543 |
| Journal | Cell Biol Int Rep |
| Year | 1988 |
| Volume | 12 |
| Pages | 927-30 |
| Authors | Holmstrom M |
| Title | Homology at a possible catalytic site in DNA topoisomerase I. |
| Related PDB | |
| Related UniProtKB | |
| [2] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1846364 |
| Journal | J Biol Chem |
| Year | 1991 |
| Volume | 266 |
| Pages | 1796-803 |
| Authors | Shuman S |
| Title |
Site-specific DNA cleavage by vaccinia virus DNA topoisomerase I. |
| Related PDB | |
| Related UniProtKB | |
| [3] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 1314832 |
| Journal | J Biol Chem |
| Year | 1992 |
| Volume | 267 |
| Pages | 8620-7 |
| Authors | Shuman S |
| Title | DNA strand transfer reactions catalyzed by vaccinia topoisomerase I. |
| Related PDB | |
| Related UniProtKB | |
| [4] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7803409 |
| Journal | Biochemistry |
| Year | 1994 |
| Volume | 33 |
| Pages | 15449-58 |
| Authors | Stivers JT, Shuman S, Mildvan AS |
| Title | Vaccinia DNA topoisomerase I: kinetic evidence for general acid-base catalysis and a conformational step. |
| Related PDB | |
| Related UniProtKB | |
| [5] | |
| Resource | |
| Comments | X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 1-77 |
| Medline ID | 95086864 |
| PubMed ID | 7994576 |
| Journal | Structure |
| Year | 1994 |
| Volume | 2 |
| Pages | 767-77 |
| Authors | Sharma A, Hanai R, Mondragon A |
| Title | Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution. |
| Related PDB | 1vcc |
| Related UniProtKB | P08585 |
| [6] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 7744804 |
| Journal | J Biol Chem |
| Year | 1995 |
| Volume | 270 |
| Pages | 11636-45 |
| Authors | Sekiguchi J, Shuman S |
| Title | Proteolytic footprinting of vaccinia topoisomerase bound to DNA. |
| Related PDB | |
| Related UniProtKB | |
| [7] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 8670847 |
| Journal | EMBO J |
| Year | 1996 |
| Volume | 15 |
| Pages | 3448-57 |
| Authors | Sekiguchi J, Shuman S |
| Title | Identification of contacts between topoisomerase I and its target DNA by site-specific photocrosslinking. |
| Related PDB | |
| Related UniProtKB | |
| [8] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9020090 |
| Journal | J Biol Chem |
| Year | 1997 |
| Volume | 272 |
| Pages | 3891-6 |
| Authors | Petersen BO, Shuman S |
| Title | Histidine 265 is important for covalent catalysis by vaccinia topoisomerase and is conserved in all eukaryotic type I enzymes. |
| Related PDB | |
| Related UniProtKB | |
| [9] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9188465 |
| Journal | J Biol Chem |
| Year | 1997 |
| Volume | 272 |
| Pages | 15721-8 |
| Authors | Sekiguchi J, Cheng C, Shuman S |
| Title | Kinetic analysis of DNA and RNA strand transfer reactions catalyzed by vaccinia topoisomerase. |
| Related PDB | |
| Related UniProtKB | |
| [10] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9224599 |
| Journal | Nucleic Acids Res |
| Year | 1997 |
| Volume | 25 |
| Pages | 3001-8 |
| Authors | Wittschieben J, Shuman S |
| Title |
Mechanism of DNA transesterification by vaccinia topoisomerase: catalytic contributions of essential residues Arg-130, |
| Related PDB | |
| Related UniProtKB | |
| [11] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9748643 |
| Journal | Biochim Biophys Acta |
| Year | 1998 |
| Volume | 1400 |
| Pages | 321-37 |
| Authors | Shuman S |
| Title | Vaccinia virus DNA topoisomerase: a model eukaryotic type IB enzyme. |
| Related PDB | |
| Related UniProtKB | |
| [12] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9529259 |
| Journal | Cell |
| Year | 1998 |
| Volume | 92 |
| Pages | 841-50 |
| Authors | Cheng C, Kussie P, Pavletich N, Shuman S |
| Title | Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. |
| Related PDB | 1a41 |
| Related UniProtKB | |
| [13] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9565576 |
| Journal | J Biol Chem |
| Year | 1998 |
| Volume | 273 |
| Pages | 11589-95 |
| Authors | Cheng C, Shuman S |
| Title | A catalytic domain of eukaryotic DNA topoisomerase I. |
| Related PDB | |
| Related UniProtKB | |
| [14] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 9421505 |
| Journal | Nucleic Acids Res |
| Year | 1998 |
| Volume | 26 |
| Pages | 490-6 |
| Authors | Wittschieben J, Petersen BO, Shuman S |
| Title |
Replacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, |
| Related PDB | |
| Related UniProtKB | |
| [15] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10047584 |
| Journal | Curr Opin Struct Biol |
| Year | 1999 |
| Volume | 9 |
| Pages | 29-36 |
| Authors | Redinbo MR, Champoux JJ, Hol WG |
| Title | Structural insights into the function of type IB topoisomerases. |
| Related PDB | |
| Related UniProtKB | |
| [16] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10911997 |
| Journal | Mol Cell |
| Year | 2000 |
| Volume | 5 |
| Pages | 1035-41 |
| Authors | Krogh BO, Shuman S |
| Title | Catalytic mechanism of DNA topoisomerase IB. |
| Related PDB | |
| Related UniProtKB | |
| [17] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 10954601 |
| Journal | Nucleic Acids Res |
| Year | 2000 |
| Volume | 28 |
| Pages | 3323-31 |
| Authors | Woodfield G, Cheng C, Shuman S, Burgin AB |
| Title | Vaccinia topoisomerase and Cre recombinase catalyze direct ligation of activated DNA substrates containing a 3'-para-nitrophenyl phosphate ester. |
| Related PDB | |
| Related UniProtKB | |
| [18] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11441004 |
| Journal | J Biol Chem |
| Year | 2001 |
| Volume | 276 |
| Pages | 36091-9 |
| Authors | Krogh BO, Shuman S |
| Title | Vaccinia topoisomerase mutants illuminate conformational changes during closure of the protein clamp and assembly of a functional active site. |
| Related PDB | |
| Related UniProtKB | |
| [19] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11756402 |
| Journal | J Biol Chem |
| Year | 2002 |
| Volume | 277 |
| Pages | 5711-4 |
| Authors | Krogh BO, Shuman S |
| Title | Proton relay mechanism of general acid catalysis by DNA topoisomerase IB. |
| Related PDB | |
| Related UniProtKB | |
| [20] | |
| Resource | |
| Comments | |
| Medline ID | |
| PubMed ID | 11830640 |
| Journal | Proc Natl Acad Sci U S A |
| Year | 2002 |
| Volume | 99 |
| Pages | 1853-8 |
| Authors | Krogh BO, Shuman S |
| Title | A poxvirus-like type IB topoisomerase family in bacteria. |
| Related PDB | |
| Related UniProtKB | |
| Comments |
|---|
|
This enzyme is composed of N-terminal region (PDB;1vcc) and C-terminal catalytic region (PDB;1a41), |
| Created | Updated |
|---|---|
| 2004-04-27 | 2009-02-26 |