PDBsum entry 2fvq

Transferase/DNA

PDB id: 2fvq

Contents

Protein chain

255 a.a. *

DNA/RNA

Waters ×130

* Residue conservation analysis

PDB id:

2fvq

Name:

Transferase/DNA

Title:

A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus

Structure:

5'-d( Cp Tp Tp Tp Cp Ap Tp Tp Ap Ap Tp Gp Ap Ap Ap G)-3'. Chain: b. Engineered: yes. Reverse transcriptase. Chain: a. Synonym: rt. Engineered: yes

Source:

Synthetic: yes. Moloney murine leukemia virus. Organism_taxid: 11801. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.30Å R-factor: 0.236 R-free: 0.263

Authors:

S.P.Montano,M.L.Cote,M.J.Roth,M.M.Georgiadis

Key ref:

S.P.Montaño et al. (2006). Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus. Nucleic Acids Res, 34, 5353-5360. PubMed id: 17003051

Date:

31-Jan-06 Release date: 12-Dec-06

Protein chain

P03355  (POL_MLVMS) -  Gag-Pol polyprotein from Moloney murine leukemia virus (isolate Shinnick)

Seq: 1738 a.a.

Struc: 255 a.a.

DNA/RNA chain

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

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.- - ?????
• Enzyme class 3: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: E.C.3.1.-.-
• Enzyme class 6: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: E.C.3.4.23.- - ?????

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

Nucleic Acids Res 34:5353-5360 (2006)

PubMed id: 17003051

Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus.

S.P.Montaño, M.L.Coté, M.J.Roth, M.M.Georgiadis.

ABSTRACT

In the first step of retroviral integration, integrase cleaves the linear viral DNA within its long terminal repeat (LTR) immediately 3' to the CA dinucleotide step, resulting in a reactive 3' OH on one strand and a 5' two base overhang on the complementary strand. In order to investigate the structural properties of the 3' end processing site within the Moloney murine leukemia virus (MMLV) LTR d(TCTTTCATT), a host-guest crystallographic method was employed to determine the structures of four self-complementary 16 bp oligonucleotides including LTR sequences (underlined), d(TTTCATTGCAATGAAA), d(CTTTCATTAATGAAAG), d(TCTTTCATATGAAAGA) and d(CACAATGATCATTGTG), the guests, complexed with the N-terminal fragment of MMLV reverse transcriptase, the host. The structures of the LTR-containing oligonucleotides were compared to those of non-LTR oligonucleotides crystallized in the same lattice. Properties unique to the CA dinucleotide step within the LTR sequence, independent of its position from the end of the duplex, include a positive roll angle and negative slide value. This propensity for the CA dinucleotide step within the MMLV LTR sequence to adopt only positive roll angles is likely influenced by the more rigid, invariable 3' and 5' flanking TT dinucleotide steps and may be important for specific recognition and/or cleavage by the MMLV integrase.