PDBsum entry 5m0r

Hydrolase

PDB id: 5m0r

Contents

Protein chains

276 a.a.

(+ 2 more) 256 a.a.

216 a.a.

205 a.a.

DNA/RNA

PDB id:

5m0r

Name:

Hydrolase

Title:

Cryo-em reconstruction of the maedi-visna virus (mvv) strand transfer complex

Structure:

Integrase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p. Fragment: unp residues 821-1101. Ec: 3.4.23.-,2.7.7.49,3.1.26.13,3.1.13.2,3.6.1.23,2.7.7.-,3.1.-.-. Engineered: yes. Vdna, non-transfered strand. Chain: q, s. Engineered: yes. Vdna-tdna, transferred strand, joined to a model tdna.

Source:

Maedi visna virus (strain kv1772). Mvv. Organism_taxid: 36374. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Visna lentivirus (strain 1514). Organism_taxid: 11742.

Authors:

V.E.Pye,A.Ballandras-Colas,D.Maskell,J.Locke,A.Kotecha,A.Costa, P.Cherepanov

Key ref:

A.Ballandras-Colas et al. (2017). A supramolecular assembly mediates lentiviral DNA integration. Science, 355, 93-95. PubMed id: 28059770 DOI: 10.1126/science.aah7002

Date:

05-Oct-16 Release date: 18-Jan-17

Protein chains

P35956  (POL_VILVK) -  Gag-Pol polyprotein from Maedi visna virus (strain KV1772)

Seq: 1506 a.a.

Struc: 276 a.a.

Protein chains

P35956  (POL_VILVK) -  Gag-Pol polyprotein from Maedi visna virus (strain KV1772)

Seq: 1506 a.a.

Struc: 256 a.a.

Protein chains

P35956  (POL_VILVK) -  Gag-Pol polyprotein from Maedi visna virus (strain KV1772)

Seq: 1506 a.a.

Struc: 216 a.a.

Protein chains

P35956  (POL_VILVK) -  Gag-Pol polyprotein from Maedi visna virus (strain KV1772)

Seq: 1506 a.a.

Struc: 205 a.a.

DNA/RNA chains

G-C-T-G-C-G-A-G-A-T-C-C-G-C-T-C-C-G-G-T-G 21 bases

C-A-C-C-G-G-A-G-C-G-G-A-T-C-T-C-G-C-A-G-T-C-G-A-C-C-A-C-C-C-T-A-A-T-C-A-A-G-T- 41 bases

A-A-A-C-T-T-G-A-T-T-A-G-G-G-T-G 16 bases

G-C-T-G-C-G-A-G-A-T-C-C-G-C-T-C-C-G-G-T-G 21 bases

C-A-C-C-G-G-A-G-C-G-G-A-T-C-T-C-G-C-A-G-T-C-G-A-C-C-A-C-C-C-T-A-A-T-C-A-A-G-T- 41 bases

A-A-A-C-T-T-G-A-T-T-A-G-G-G-T-G 16 bases

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.3.1.-.-
• Enzyme class 5: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 6: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.3.4.23.- - ?????
• Enzyme class 8: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.3.6.1.23 - dUTP diphosphatase.
• Reaction: dUTP + H2O = dUMP + diphosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1126/science.aah7002

Science 355:93-95 (2017)

PubMed id: 28059770

A supramolecular assembly mediates lentiviral DNA integration.

A.Ballandras-Colas, D.P.Maskell, E.Serrao, J.Locke, P.Swuec, S.R.Jónsson, A.Kotecha, N.J.Cook, V.E.Pye, I.A.Taylor, V.Andrésdóttir, A.N.Engelman, A.Costa, P.Cherepanov.

ABSTRACT

No abstract given.