1D0E

CRYSTAL STRUCTURES OF THE N-TERMINAL FRAGMENT FROM MOLONEY MURINE LEUKEMIA VIRUS REVERSE TRANSCRIPTASE COMPLEXED WITH NUCLEIC ACID: FUNCTIONAL IMPLICATIONS FOR TEMPLATE-PRIMER BINDING TO THE FINGERS DOMAIN

PDB DOI: 10.2210/pdb1D0E/pdb
NDB: PD0135

Classification: TRANSFERASE/DNA
Organism(s): Moloney murine leukemia virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-09-09 Released: 2000-04-04
Deposition Author(s): Najmudin, S., Cote, M.L., Sun, D., Yohannan, S., Montano, S.P., Gu, J., Georgiadis, M.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.298
R-Value Work: 0.215
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

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

(2000) J Mol Biol 296: 613-632

PubMed: 10669612 Search on PubMed
DOI: 10.1006/jmbi.1999.3477
Primary Citation of Related Structures:
1D0E, 1QAI, 1QAJ

PubMed 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.

Related Citations:

Cloning, expression and purification of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase: Crystallization of nucleic acid complexes
Sun, D., Jessen, S., Liu, C., Liu, X., Najmudin, S., Georgiadis, M.
(1998) Protein Sci 7: 1575

Organizational Affiliation:

Waksman Institute, Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE	C [auth A], D [auth B]	259	Moloney murine leukemia virus	Mutation(s): 0 Gene Names: MMLV-RT EC: 2.7.7.49 (PDB Primary Data), 3.4.23 (UniProt), 2.7.7.7 (UniProt), 3.1.26.4 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick)) Explore P03355 Go to UniProtKB: P03355
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03355
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Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(TPTPTPCPAPTPGPCPAPTP*G)-3'	A [auth E], B [auth F]	11	N/A
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Reference Sequence