PDBsum entry 1qai

Transferase/DNA

PDB id: 1qai

Contents

Protein chains

251 a.a. *

DNA/RNA

Metals

_HG ×4

Waters ×281

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structures of an n-Terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-Primer binding to the fingers domain.

Authors

S.Najmudin, M.L.Coté, D.Sun, S.Yohannan, S.P.Montano, J.Gu, M.M.Georgiadis.

Ref.

J Mol Biol, 2000, 296, 613-632. [DOI no: 10.1006/jmbi.1999.3477]

PubMed id

10669612

Abstract

Reverse transcriptase (RT) serves as the replicative polymerase for retroviruses by using RNA and DNA-directed DNA polymerase activities coupled with a ribonuclease H activity to synthesize a double-stranded DNA copy of the single-stranded RNA genome. In an effort to obtain detailed structural information about nucleic acid interactions with reverse transcriptase, we have determined crystal structures at 2.3 A resolution of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed to blunt-ended DNA in three distinct lattices. This fragment includes the fingers and palm domains from Moloney murine leukemia virus reverse transcriptase. We have also determined the crystal structure at 3.0 A resolution of the fragment complexed to DNA with a single-stranded template overhang resembling a template-primer substrate. Protein-DNA interactions, which are nearly identical in each of the three lattices, involve four conserved residues in the fingers domain, Asp114, Arg116, Asn119 and Gly191. DNA atoms involved in the interactions include the 3'-OH group from the primer strand and minor groove base atoms and sugar atoms from the n-2 and n-3 positions of the template strand, where n is the template base that would pair with an incoming nucleotide. The single-stranded template overhang adopts two different conformations in the asymmetric unit interacting with residues in the beta4-beta5 loop (beta3-beta4 in HIV-1 RT). Our fragment-DNA complexes are distinct from previously reported complexes of DNA bound to HIV-1 RT but related in the types of interactions formed between protein and DNA. In addition, the DNA in all of these complexes is bound in the same cleft of the enzyme. Through site-directed mutagenesis, we have substituted residues that are involved in binding DNA in our crystal structures and have characterized the resulting enzymes. We now propose that nucleic acid binding to the fingers domain may play a role in translocation of nucleic acid during processive DNA synthesis and suggest that our complex may represent an intermediate in this process.

Figure 5.
Figure 5. Superpositionings of the higher-resolution structures at the DNA binding site. In both views the backgrounded DNA molecule is that of form IV, and the ion-pair formed between Asp114 and Arg116 in form IV is shown with black dashes. Both views also show smaller bonds and atoms for the dual conformations of Tyr64 of form IV. Superpositionings were done using the same subset of alpha-carbon atoms listed for Figure 2. (a) The superpositioning of the A and B protein molecules of form I onto that of form IV. The main-chains and side-chains nearly superimpose with the exception of the main-chain of the form I B molecule in the region of Tyr64. (b) Superpositioning of the A and B protein molecules of form IIa onto that of form IV. The main and side-chain superpositionings are nearly identical for the residues shown, and there is an exact mapping of the Asp114 side-chain of the form IIa A molecule and that of form IV.

Figure 7.
Figure 7. Stereodiagrams of DNA bound to the fingers domain of the MMLV RT fragment as modeled in the previously defined binding cleft in HIV-1 RT. (a) A trace rendering shows the fragment of MMLV RT in blue including the fingers and palm domains superimposed on the fingers, palm, and thumb domains from HIV-1 RT (2hmi structure) [Ding et al 1998]. DNA as bound to the fingers domain in form IIb crystals is shown as a stick model in red. The superpositioning of the fingers and palm domains from MMLV RT and HIV-1 RT is based on the 160 most similar residues as reported by [Georgiadis et al 1995] and listed in the legend in Figure 2. (b) The same molecules are superimposed as in (a). The DNA shown in red from the HIV-1 RT-DNA-Fab complex structure (2hmi) is shown for comparison in a similar view along the cleft formed by the fingers, palm, and thumb domains.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 296, 613-632) copyright 2000.

Secondary reference #1

Title

Cloning, Expression, And purification of a catalytic fragment of moloney murine leukemia virus reverse transcriptase: crystallization of nucleic acid complexes.

Authors

D.Sun, S.Jessen, C.Liu, X.Liu, S.Najmudin, M.M.Georgiadis.

Ref.

Protein Sci, 1998, 7, 1575-1582. [DOI no: 10.1002/pro.5560070711]

PubMed id

9684890

Figure 1.
Fig. 1. Oligonucleotide sequences complexed with catalytic fragment are shown. The sequences are identified y primer/template lengths. The 8/14. mer sequence mentioned n Results is from the 8/16-mer sequence and lacks the 5' CT found in the 16-mer sequence.

Figure 2.
Fig. 2. Microseeded crystals grown in the presence of A) 16/16-mer. (R) 8/16-mer, (C) 8/8-mer are shown. Both /16-mer and 8/8-mr crystals have been characterized nd shown to be Form I crystals. (D) Microseeded Form 111 crystals grown with /10-mer to catalytic fragment are shown. (E) Typical Form I1 crystals obtained by microseeding are shown.

The above figures are reproduced from the cited reference which is an Open Access publication published by the Protein Society