Conformational Structure of Unliganded Reverse Transcriptase

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Reverse transcriptase is a polymerase that is able to make a complimentary DNA strand from an RNA template. It is also able to then polymerize the single stranded cDNA into a double stranded molecule. Reverse transciptases are usually found in retroviruses, which use RT to make a DNA copy of their own RNA genome, which is then incorporated into the host cell's genome. While there are several different kinds of reverse transcriptases, the purpose of this chime tutorial is to highlight the key conformational and structural features of the human immunodeficiency virus-1 (HIV-1) reverse transcriptase and show how they function in enzymatic activity. For more background information on HIV-1 reverse transcriptase, click here. This chime tutorial is best viewed if the buttons are pressed in sequence. If you do not have the chime plugin, you can download it here. This button will be the reset view for the chime tutorial.

To begin, let's take a brief tour of the conformational shape and structure of reverse transcriptase.

HIV-1 reverse transcriptase is a heterodimer protein (composed of 2 different polypeptides) that has a 66 kDa subunit (p66) and a 51 kDa subunit (p51) (Hsiou et al., 1996). Subunits
p66 and p51 have identical amino acid sequences, but subunit p51 is a cleaved version of p66. Furthermore, although the amino acid sequences are the same, the structural conformation of the two subunits is significantly different (Goldman & Marcey, 2001). Each subunit can be further divided into four subdomains: the fingers, thumb, palm, and connection. In addition, subunit p66 has an additional RNAse H subdomain. While both the p51 and p66 subunits are necessary for reverse transcriptase, this tutorial will focus mainly on the p66 subunit because it has the polymerase active site and is responsible for a majority of the enzymatic function.

thumb and fingers subdomains of the p66 subunit serve as a clamp to hold RNA in the polymerase active site of the palm subdomain (Goldman & Marcey, 2001). The RNase H subdomain cleaves the RNA template once the cDNA strand has been polymerized. A magnesium ion is embedded within the RNase H subdomain and interacts with aspartic acids 443, 498, and 549. While the specific function of this ion is unclear, it is thought to play a role in the DNA cleavage process (Ren et al., 1995). The polymerase active site is located within the palm subdomain and is where DNA synthesis from the RNA template occurs. A trio of aspartic acid residues (110, 185, 186) at the polymerase active site ligate two metal ions (possibly magnesium), which interact with the phosphates of the DNA primer and incorporated nucleotides (Doublie, Sawaya, & Ellenberger, 1999). Now view reverse transcriptase complete with all it's functional subdomains and motifs.

Let's take a closer look now at how the conformational structure of reverse transcriptase specifically functions to polymerize a DNA molecule from a nucleic acid template.


Doublie S, Sawaya MR, Ellenberger T. 1999. An open and closed case for all polymerases. Structure (7)2. <http://www.sciencedirect
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Goldman M, Marcey D. 2001. HIV-1 Reverse Transcriptase. The Online Molecular Museum. <
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Hsiou Y, Ding J, Das K, Clark, Jr AD, Hughes SH, Arnold E. 1996. Structure of unliganded HIV-1 reverse transcriptase at 2.7 A resolution: implications of conformational changes for polymeraztion and inhibition mechanisms. Structure 4(7). <
> Accessed 2005 Feb 12.

Ren J, Esnouf R, Hopkins A, Ross C, Jones Y, Stammers D, Stuart D. 1995. The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design. Structure 3(9). <
>. Accessed 2005 Feb 12