1RDH

CRYSTALLOGRAPHIC ANALYSES OF AN ACTIVE HIV-1 RIBONUCLEASE H DOMAIN SHOW STRUCTURAL FEATURES THAT DISTINGUISH IT FROM THE INACTIVE FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å

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This is version 1.3 of the entry. See complete history

Literature

Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form.

Chattopadhyay, D.Finzel, B.C.Munson, S.H.Evans, D.B.Sharma, S.K.Strakalaitus, N.A.Brunner, D.P.Eckenrode, F.M.Dauter, Z.Betzel, C.Einspahr, H.M.

(1993) Acta Crystallogr.,Sect.D 49: 423-427

  • DOI: 10.1107/S0907444993002409

  • PubMed Abstract: 
  • . An active recombinant preparation of the carboxy-terminal ribonuclease H (RNase H) domain of HIV-I reverse transcriptase has produced crystals of several different forms, including a trigonal prism form (P3(1); a = b = 52.03, c = 113.9 A with two m ...

    . An active recombinant preparation of the carboxy-terminal ribonuclease H (RNase H) domain of HIV-I reverse transcriptase has produced crystals of several different forms, including a trigonal prism form (P3(1); a = b = 52.03, c = 113.9 A with two molecules per asymmetric unit) and a hexagonal tablet form (P6(2)22 or P6(4)22; a = b = 93.5, c = 74.1 A with one molecule per asymmetric unit). The former appears to be isomorphous with crystals of a similar, but inactive, version of the enzyme that was used for a prior crystal structure determination [Davies, Hostomska, Hostomsky, Jordan & Matthews (1991). Science, 252, 88-95]. We have also obtained a structure solution for this crystal form and have refined it with 2.8 A resolution data (R = 0.216). We report here details of our crystallization studies and some initial structural results that verify that the preparation of active HIV-1 RNase H yields a protein that is not just enzymatically, but also structurally, distinguishable from the inactive form. Evidence suggests that region 538-542, which may be involved in the catalytic site and which is disordered in both molecules in the prior structure determination, is ordered in the crystal structure of the active enzyme, although the ordering may include more than one conformation for this loop. It should also be noted that, in the crystal structure of the trigonal form, RNase H monomers associate to form noncrystallographic twofold-symmetric dimers by fusing five-stranded mixed beta sheets into a single ten-stranded dimerwide sheet, an assembly that was not remarked upon by previous investigators.


    Related Citations: 
    • A Recombinant Ribonuclease H Domain of HIV-1 Reverse Transcriptase that is Enzymatically Active
      Evans, D.B.,Brawn, K.,Deibel Junior, M.R.,Tarpley, W.G.,Sharma, S.K.
      (1991) J.Biol.Chem. 266: 20583
    • Crystal Structure of the Ribonuclease H Domain of HIV-1 Reverse Transcriptase
      Davies II, J.F.,Hostomska, Z.,Hostomsky, Z.,Jordan, S.R.,Matthews, D.A.
      (1991) Science 252: 88


    Organizational Affiliation

    The Upjohn Company, Kalamazoo, Michigan 49001, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 REVERSE TRANSCRIPTASE (RIBONUCLEASE H DOMAIN)
A, B
146Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 52.030α = 90.00
b = 52.030β = 90.00
c = 113.920γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other