RT/RNase H (Reverse Transcriptase and RNase H)

HIV RT/RNase H forms a heterodimer with RT/RNase H polyprotein and reverse transcribes viral RNA into DNA.





PDB-1RTD: HIV-1 (isolate UNKNOWN) RT mutant (UNKNOWN) and DNA complex - produced using SwissModel/SPDBV/POVray
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PDB: 1RTD (HIV-1 RT)
SwissProt: P04585 (HIV-1 HXB2 POL)
Chime Tutorial: not available
Los Alamos HIV structure DB: Reverse Transcriptase
EMBL: K03455 [EMBL/GenBank/DDBJ]
BioAfrica: Pol Protein Data Mining Tool


Isoforms:

Cleavage site:

Localization:

  • Virion
  • Cell cytoplasm

Function:

  • RT makes a double-stranded DNA copy of the dimer of single-stranded RNA
  • RT has both RNA-dependant and DNA-dependant polymerase activity
  • RNase H activity removes RNA strand from RNA/DNA duplex

Additional Information:

  • RT has low fidelity (high frequency of mutation)
  • viral DNA can be completely synthesized within 6 hours of viral entry
  • major functional species of polymerase is a heterodimer of p50 (Reverse Transcriptase) and p65 (Reverse Transcriptase - RNase H) (Ref. #2)
  • many cis-acting elements in viral RNA are required for the generation of viral DNA (Ref. #3)
  • TAR is a small RNA stem-loop structure located at 5'-end of viral RNA and is required for initiation of Reverse Transcriptase (Ref. #3)

Genomic Location: [TOP]

Reference Sequences:

HIV-1 (HXB2):

          10         20         30         40         50         60         70 
| | | | | | |
PISPIETVPV KLKPGMDGPK VKQWPLTEEK IKALVEICTE MEKEGKISKI GPENPYNTPV FAIKKKDSTK
80 90 100 110 120 130 140
| | | | | | |
WRKLVDFREL NKRTQDFWEV QLGIPHPAGL KKKKSVTVLD VGDAYFSVPL DEDFRKYTAF TIPSINNETP
150 160 170 180 190 200 210
| | | | | | |
GIRYQYNVLP QGWKGSPAIF QSSMTKILEP FRKQNPDIVI YQYMDDLYVG SDLEIGQHRT KIEELRQHLL
220 230 240 250 260 270 280
| | | | | | |
RWGLTTPDKK HQKEPPFLWM GYELHPDKWT VQPIVLPEKD SWTVNDIQKL VGKLNWASQI YPGIKVRQLC
290 300 310 320 330 340 350
| | | | | | |
KLLRGTKALT EVIPLTEEAE LELAENREIL KEPVHGVYYD PSKDLIAEIQ KQGQGQWTYQ IYQEPFKNLK
360 370 380 390 400 410 420
| | | | | | |
TGKYARMRGA HTNDVKQLTE AVQKITTESI VIWGKTPKFK LPIQKETWET WWTEYWQATW IPEWEFVNTP
430 440 450 460 470 480 490
| | | | | | |
PLVKLWYQLE KEPIVGAETF YVDGAANRET KLGKAGYVTN RGRQKVVTLT DTTNQKTELQ AIYLALQDSG
500 510 520 530 540 550 560
| | | | | | |
LEVNIVTDSQ YALGIIQAQP DQSESELVNQ IIEQLIKKEK VYLAWVPAHK GIGGNEQVDK LVSAGIRKVL
[download in fasta format]
Length: 560 amino acids (residues 155 to 715)
Molecular Weight: 64479 Da
Theoretical pI: 8.57




Primary and Secondary Database Entries: [TOP]

Identifiers:

PDB: Search for HIV & p66

SwissProt: P04585 (HIV-1 HXB2 POL)
EMBL: K03455; AAB50259.1 [EMBL/GenBank/DDBJ]

PIR: UNKNOWN
HIV: K03455; UNKNOWN$HXB2
InterPro: IPR008187;UNKNOWN
Pfam: PF00558;UNKNOWN
Prints: none
ProDom: PD000472
SCOP: SSF56672; DNA/RNA polymerase / SSF53098; Ribonuclease H-like
BLOCKS: P04585
Prosite: P04585
ProtoNet: P04585
ProtoMap: P04585
PRESAGE: P04585
Database of Interacting Proteins: P04585
ModBase: P04585
Swiss-2DPAGE: 2D gel

BioAfrica Tools:
- Pol Protein Data Mining Tool provides real-time analysis of HIV-1 Pol isolates
- HIV Structure BLAST searches for similar HIV sequences that have known structures
- HIV Proteomics Resource contains protein sequence and structure analysis tools
Reviews and References: [TOP]


Cite the resource by citing the following paper:
Doherty R et al. BioAfrica's HIV-1 Proteomics Resource: Combining protein data with bioinformatics tools. Retrovirology (2005), 9;2(1):18.

0 - HIV Sequence Compendium 2000
Kuiken CL, Foley B, Hahn B, Korber B, Marx PA, McCutchan F, Mellors JW, Mullins JI, Sodroski J, Wolinksy S.
Theoretical Biol. & Biophys. Group, Los Alamos Nat Lab, LA-UR 01-3860 [Read it online: Compendium]
0 - Retroviruses
Coffin JM, Hughes SH, Varmus HE.
CD-ROM ed. (2002) Cold Spring Harbor Laboratory Press [Read it online: NCBI Bookshelf]
1 - Molecular Characteristics of HIV-1 Subtype C Viruses from KwaZulu-Natal, South Africa:
Implications for Vaccine and Antiretroviral Control Strategies.
Gordon M, De Oliveira T, Bishop K, Coovadia HM, Madurai L, Engelbrecht S, Janse van Rensburg E, Mosam A, Smith A, Cassol S.
Journal of Virology 77(4): 2587-2599 (2003) [pubmed: 12551997]
2 - Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor.
Kohlstaedt LA, Wang J, Friedman JM.
Science 256: 1783-1790 (1992) [pubmed: 1377403]
3 - A critical role for the TAR element in promoting efficient human immunodeficiency virus type 1
reverse transcription.
Harrich D, Ulich C, Gaynor RB.
J Virol 70: 4017-4127 (1996) [pubmed: 8648739]





Page last updated by Tulio de Oliveira.