2HMI

HIV-1 REVERSE TRANSCRIPTASE/FRAGMENT OF FAB 28/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.352 
  • R-Value Work: 0.271 

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This is version 1.2 of the entry. See complete history


Literature

Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution.

Ding, J.Das, K.Hsiou, Y.Sarafianos, S.G.Clark Jr., A.D.Jacobo-Molina, A.Tantillo, C.Hughes, S.H.Arnold, E.

(1998) J Mol Biol 284: 1095-1111

  • DOI: 10.1006/jmbi.1998.2208
  • Primary Citation of Related Structures:  
    2HMI

  • PubMed Abstract: 
  • The structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexed with a 19-mer/18-mer double-stranded DNA template-primer (dsDNA) and the Fab fragment of monoclonal antibody 28 (Fab28) has been refined at 2.8 A resolution ...

    The structure of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) complexed with a 19-mer/18-mer double-stranded DNA template-primer (dsDNA) and the Fab fragment of monoclonal antibody 28 (Fab28) has been refined at 2.8 A resolution. The structures of the polymerase active site and neighboring regions are described in detail and a number of novel insights into mechanisms of polymerase catalysis and drug inhibition are presented. The three catalytically essential amino acid residues (Asp110, Asp185, and Asp186) are located close to the 3' terminus of the primer strand. Observation of a hydrogen bond between the 3'-OH of the primer terminus and the side-chain of Asp185 suggests that the carboxylate of Asp185 could act as a general base in initiating the nucleophilic attack during polymerization. Nearly all of the close protein-DNA interactions involve atoms of the sugar-phosphate backbone of the nucleic acid. However, the phenoxyl side-chain of Tyr183, which is part of the conserved YMDD motif, has hydrogen-bonding interactions with nucleotide bases of the second duplex base-pair and is predicted to have at least one hydrogen bond with all Watson-Crick base-pairs at this position. Comparison of the structure of the active site region in the HIV-1 RT/dsDNA complex with all other HIV-1 RT structures suggests that template-primer binding is accompanied by significant conformational changes of the YMDD motif that may be relevant for mechanisms of both polymerization and inhibition by non-nucleoside inhibitors. Interactions of the "primer grip" (the beta12-beta13 hairpin) with the 3' terminus of the primer strand primarily involve the main-chain atoms of Met230 and Gly231 and the primer terminal phosphate. Alternative positions of the primer grip observed in different HIV-1 RT structures may be related to conformational changes that normally occur during DNA polymerization and translocation. In the vicinity of the polymerase active site, there are a number of aromatic residues that are involved in energetically favorable pi-pi interactions and may be involved in the transitions between different stages of the catalytic process. The protein structural elements primarily responsible for precise positioning of the template-primer (including the primer grip, template grip, and helices alphaH and alphaI of the p66 thumb) can be thought of functioning as a "translocation track" that guides the relative movement of nucleic acid and protein during polymerization.


    Related Citations: 
    • Structure of Unliganded HIV-1 Reverse Transcriptase at 2.7 A Resolution: Implications of Conformational Changes for Polymerization and Inhibition Mechanisms
      Hsiou, Y., Ding, J., Das, K., Clark Junior, A.D., Hughes, S.H., Arnold, E.
      (1996) Structure 4: 853
    • Crystallization of Human Immunodeficiency Virus Type 1 Reverse Transcriptase with and without Nucleic Acid Substrates, Inhibitors, and an Antibody Fab Fragment
      Clark Junior, A.D., Jacobo-Molina, A., Clark, P., Hughes, S.H., Arnold, E.
      (1995) Methods Enzymol 262: 171
    • Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
      Ding, J., Das, K., Tantillo, C., Zhang, W., Clark Junior, A.D., Jessen, S., Lu, X., Hsiou, Y., Jacobo-Molina, A., Andries, K., Pauwels, R., Moereels, H., Koymans, L., Janssen, P.A.J., Smith Junior, R.H., Koepke, M.K., Michejda, C.J., Hughes, S.H., Arnold, E.
      (1995) Structure 3: 365
    • Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors
      Ding, J., Das, K., Moereels, H., Koymans, L., Andries, K., Janssen, P.A., Hughes, S.H., Arnold, E.
      (1995) Nat Struct Biol 2: 407
    • Crystal Structure of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Complexed with Double-Stranded DNA at 3.0 A Resolution Shows Bent DNA
      Jacobo-Molina, A., Ding, J., Nanni, R.G., Clark Junior, A.D., Lu, X., Tantillo, C., Williams, R.L., Kamer, G., Ferris, A.L., Clark, P., Hizi, A., Hughes, S.H., Arnold, E.
      (1993) Proc Natl Acad Sci U S A 90: 6320
    • Structure of HIV-1 Reverse Transcriptase/DNA Complex at 7 A Resolution Showing Active Site Locations
      Arnold, E., Jacobo-Molina, A., Nanni, R.G., Williams, R.L., Lu, X., Ding, J., Clark Junior, A.D., Zhang, A., Ferris, A.L., Clark, P., Hizi, A., Hughes, S.H.
      (1992) Nature 357: 85

    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ, 08854-5638, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SUBUNIT OF V-1 REVERSE TRANSCRIPTASEC [auth A]558Human immunodeficiency virus 1Mutation(s): 1 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
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Go to UniProtKB:  P03366
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HISUBUNIT OF V-1 REVERSE TRANSCRIPTASED [auth B]430Human immunodeficiency virus 1Mutation(s): 1 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENT OF MONOCLONAL ANTIBODY 28E [auth C]214Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENT OF MONOCLONAL ANTIBODY 28F [auth D]220Mus musculusMutation(s): 0 
Protein Feature View
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3')A [auth E]19N/A
    Protein Feature View
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3')B [auth F]18N/A
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      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.352 
      • R-Value Work: 0.271 
      • Space Group: P 32 1 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 169α = 90
      b = 169β = 90
      c = 221γ = 120
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      X-PLORrefinement

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 1998-04-10 
      • Released Date: 1998-10-14 
      • Deposition Author(s): Ding, J., Arnold, E.
      • This entry supersedes: 1HMI

      Revision History  (Full details and data files)

      • Version 1.0: 1998-10-14
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance