RNase H

HIV RNase H removes the original RNA template from the first DNA strand allowing synthesis of the complementary strand of DNA.

PDB-1o1w: HIV-1 (isolate UNKNOWN) RNase H - produced using SwissModel/SPDBV/POVray
[animated gif: 320x240 ]
ViralZone:HIV-1
PDB: 1o1w (HIV-1 RNase H)
SwissProt: P04585 (HIV-1 HXB2 POL)
Chime Tutorial:  not available
Los Alamos HIV structure DB: not available
EMBL: K03455 [EMBL/GenBank/DDBJ]
BioAfrica: Pol Protein Data Mining Tool


Isoforms:

  • p15 (120 amino acids)


Cleavage site:


Localization:

  • Virion
  • Cell cytoplasm


Function:

  • Removes RNA template strand from RNA/DNA duplex

Additional Information:

  • none

Genomic Location: [TOP]

Reference Sequences:

HIV-1 (HXB2): 

          10         20         30         40         50         60         70 
           |          |          |          |          |          |          | 
  YVDGAANRET KLGKAGYVTN RGRQKVVTLT DTTNQKTELQ AIYLALQDSG LEVNIVTDSQ YALGIIQAQP
          80         90        100        110        120 
           |          |          |          |          | 
  DQSESELVNQ IIEQLIKKEK VYLAWVPAHK GIGGNEQVDK LVSAGIRKVL 
      [download in fasta format]

Length: 120 amino acids (residues 595 - 715)
Molecular Weight: 13167 Da
Theoretical pI: 6.8
Protein Domains/Folds/Motifs: [TOP]

InterPro signature for RNase H - IPR002156



Secondary Structure prediction:

Antigenic Sites - EMBOSS:
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]

  • Viral RNA
Primary and Secondary Database Entries: [TOP]

Identifiers:

ViralZone: HIV-1
PDB/MMDB: Search for HIV-1 & Ribonuclease H

SwissProt: P04585 (HIV-1 HXB2 POL)
EC: 3.1.26.4
EMBL: K03455; AAB50259.1 [EMBL/GenBank/DDBJ]

PIR: UNKNOWN
HIV: K03455; UNKNOWN$HXB2
InterPro: IPR002156
Pfam: PF00075
Prints: none
ProDom: PD000727 (1 - 66) / PD106055 (36 - 119) / PD390352 (39 - 110) / PD416714 (69 - 109)
PD582846 (80 - 117) / PD685225 (81 - 110)
SCOP: SSF53098 RNase H-like protein
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.

1 - 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]
2 - Retroviruses
Coffin JM, Hughes SH, Varmus HE.
CD-ROM ed. (2002) Cold Spring Harbor Laboratory Press [Read it online: NCBI Bookshelf]
3 - 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]



Page last updated by Tulio de Oliveira.