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

RT/RNase H (Reverse Transcriptase and RNase H)


Description:

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

Isoforms:

Cleavage site:

Localization:

  • virion
  • 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
Protein Domains/Folds/Motifs: [TOP]

InterPro signature for XXXXX - XXXXX




Predicted Motifs: Printer-friendly version
N-glycosylation:
N-myristoylation:
Amidation:
Protein kinase C:
Casein kinase II:
Tyrosine kinase:
cAMP / cGMP kinase:
Cell attachment motif:
Asp Protease motif:
Asp Prot Retro motif:
Cysteine-rich Region:
Tryptophan-rich Region:
Zinc-finger CCHC motif:
Leucine Zipper motif:

Protein-Protein Interactions: [TOP]

  • XXXXX interacts at residues XXXXX and XXXXX.
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]

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: XXXXXXXXXX]
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: XXXXXXXXXX]

The HIV-1 Proteome is a section of the BioAfrica Proteomics Resource.
If you have any questions, comments or suggestions, please contact me at rdoherty@mrc.ac.za.

Keywords: phosphorylation; virion; nucleus; Reverse Transcriptase; RT; accessory protein; membrane protein; HIV; AIDS; HIV Reverse Transcriptase; HIV RT

Developed by:
Ryan Doherty¹, Tulio de Oliveira¹, Siva Danaviah¹, Michelle Gordon¹, Chris Seebregts², and Sharon Cassol¹.
Molecular Virology and Bioinformatics Unit of Africa Centre for Health and Populations Studies Nelson R Mandela School of Medicine, University of Natal¹, and the Research Information Systems Division, South African Medical Research Council (MRC)².

Revised 16 of Sept 2003 - Copyright © 2003 Africa Centre - All Rights Reserved.