PDBsum entry 1rdh

Hydrolase(endoribonuclease)

PDB id: 1rdh

Contents

Protein chains

127 a.a.* *

* Residue conservation analysis

* C-alpha coords only

PDB id:

1rdh

Name:

Hydrolase(endoribonuclease)

Title:

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

Structure:

HIV-1 reverse transcriptase (ribonuclease h domain). Chain: a, b. Engineered: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.80Å R-factor: 0.215

Authors:

B.C.Finzel,D.Chattopadhyay,H.M.Einspahr

Key ref:

D.Chattopadhyay et al. (1993). Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form. Acta Crystallogr D Biol Crystallogr, 49, 423-427. PubMed id: 15299518 DOI: 10.1107/S0907444993002409

Date:

05-Mar-93 Release date: 31-May-94

Protein chains

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 127 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.1.-.-
• Enzyme class 5: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 6: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444993002409

Acta Crystallogr D Biol Crystallogr 49:423-427 (1993)

PubMed id: 15299518

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

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

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 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.

Selected figure(s)

Figure 1.
Fig. 1. Stylized ribbon representations of the two HIV-1 RNase H domains found in the crystallographic asymmetric unit. The two dmains are related by noncrystallographic twofold axis that is normal to the figure in view (a) and horizontal in the plane of the page in view (b). The two monomers interact at the outermost strand (~3) of the five-stranded ~ sheet to form a single large sheet that spans both domains. The position of His539 is indicated.

The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 423-427) copyright 1993.

Figure was selected by an automated process.