1i6j
From Proteopedia
CRYSTAL STRUCTURE OF A PSEUDO-16-MER DNA WITH STACKED GUANINES AND TWO G-A MISPAIRS COMPLEXED WITH THE N-TERMINAL FRAGMENT OF MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE
Structural highlights
FunctionPOL_MLVMS Gag-Pol polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release. Matrix protein p15 targets Gag and gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell (By similarity). Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral dimeric RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA binds to the primer-binding site (PBS) situated at the 5' end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5' end of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primers. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step that requires cell division, the PIC enters cell nucleus. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The last step is viral DNA integration into host chromosome (By similarity). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe X-ray crystal structure at 2.0 A resolution of a DNA molecule complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) has been determined. This method allows the study of nucleic acids in a unique and largely unfettered environment without the complicated lattice interactions typically observed in DNA-only crystal structures. Molecular-replacement phasing using only the protein provided readily interpretable electron density with no model bias for the DNA. The asymmetric unit of the structure consists of the protein molecule bound to the blunt end of a DNA 6/10-mer, which is composed of a six-base strand (5'-GTCGTC-3') and a ten-base strand (3'-CAGCAGGGCA-5'), resulting in a six-base-pair duplex with a four-base single-stranded overhang. In the crystal structure, the bases of the overhang reciprocally pair to yield a doubly nicked pseudo-hexadecamer primarily B-form DNA molecule. The pairing between the single strands gives two standard (G-C) Watson-Crick pairs and two G(anti)-A(anti) mispairs. The mispairs reside in a G-C-rich environment and the three consecutive guanines on the 10-mer impart interesting structural features to the pseudo-hexadecamer, such as the preference for a guanine stack, stretching the C-G base pairs flanking the mispair to the point of loss of intra-base-pair hydrogen bonding. The DNA was designed for the purpose of comparison with a previous structure, which was determined in the same crystal lattice. In all of the authors' previous fragment-DNA complexes, the nucleotide at the blunt-ended 3'-hydroxyl was a purine. Consistent with the proposed mechanistic role of interactions with the 3'-hydroxyl in processive DNA synthesis by RT, it was found that a pyrimidine at this position in the DNA makes indentical interactions with the strictly conserved Gly191 and the main chain of Leu115 of MMLV RT. Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase.,Cote ML, Georgiadis MM Acta Crystallogr D Biol Crystallogr. 2001 Sep;57(Pt 9):1238-50. Epub 2001, Aug 23. PMID:11526315[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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