PMID- 33214855
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20201121
IS  - 1985-3718 (Print)
IS  - 2180-4249 (Electronic)
IS  - 1985-3718 (Linking)
VI  - 31
IP  - 3
DP  - 2020 Oct
TI  - Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus 
      Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus 
      Monkey.
PG  - 47-61
LID - 10.21315/tlsr2020.31.3.4 [doi]
AB  - Simian betaretrovirus serotype-2 (SRV-2) is an important pathogenic agent in 
      Asian macaques. It is a potential confounding variable in biomedical research. 
      SRV-2 also provides a valuable viral model compared to other retroviruses which 
      can be used for understanding many aspects of retroviral-host interactions and 
      immunosuppression, infection mechanism, retroviral structure, antiretroviral and 
      vaccine development. In this study, we isolated the gene encoding reverse 
      transcriptase enzyme (RT) of SRV-2 that infected Indonesian cynomolgus monkey (Mf 
      ET1006) and predicted the three dimensional structure model using the iterative 
      threading assembly refinement (I-TASSER) computational programme. This SRV-2 RT 
      Mf ET1006 consisted of 547 amino acids at nucleotide position 3284-4925 of whole 
      genome SRV-2. The polymerase active site located in the finger/palm subdomain 
      characterised by three conserved catalytic aspartates (Asp90, Asp165, Asp166), 
      and has a highly conserved YMDD motif as Tyr163, Met164, Asp165 and Asp166. We 
      estimated that this SRV-2 RT Mf ET1006 structure has the accuracy of template 
      modelling score (TM-score 0.90 +/- 0.06) and root mean square deviation (RMSD) 4.7 
      +/- 3.1A, indicating that this model can be trusted and the accuracy can be seen 
      from the appearance of protein folding in tertiary structure. The 
      superpositionings between SRV-2 RT Mf ET1006 and Human Immunodeficiency Virus-1 
      (HIV-1) RT were performed to predict the structural in details and to optimise 
      the best fits for illustrations. This SRV-2 RT Mf ET1006 structure model has the 
      highest homology to HIV-1 RT (2B6A.pdb) with estimated accuracy at TM-score 
      0.911, RMSD 1.85 A, and coverage of 0.953. This preliminary study of SRV-2 RT Mf 
      ET1006 structure modelling is intriguing and provide some information to explore 
      the molecular characteristic and biochemical mechanism of this enzyme.
CI  - (c) Penerbit Universiti Sains Malaysia, 2020.
FAU - Saepuloh, Uus
AU  - Saepuloh U
AD  - Primate Research Centre, Bogor Agricultural University (PSSP LPPM IPB), Jalan 
      Lodaya II/5 Bogor 16151, Indonesia.
FAU - Iskandriati, Diah
AU  - Iskandriati D
AD  - Primate Research Centre, Bogor Agricultural University (PSSP LPPM IPB), Jalan 
      Lodaya II/5 Bogor 16151, Indonesia.
FAU - Pamungkas, Joko
AU  - Pamungkas J
AD  - Primate Research Centre, Bogor Agricultural University (PSSP LPPM IPB), Jalan 
      Lodaya II/5 Bogor 16151, Indonesia.
AD  - Faculty of Veterinary Medicine, Bogor Agricultural University, Kampus Darmaga, 
      Bogor 16680, Indonesia.
FAU - Solihin, Dedy Duryadi
AU  - Solihin DD
AD  - Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor 
      Agricultural University, Kampus Darmaga, Bogor 16680, Indonesia.
FAU - Mariya, Sela Septima
AU  - Mariya SS
AD  - Primate Research Centre, Bogor Agricultural University (PSSP LPPM IPB), Jalan 
      Lodaya II/5 Bogor 16151, Indonesia.
FAU - Sajuthi, Dondin
AU  - Sajuthi D
AD  - Primate Research Centre, Bogor Agricultural University (PSSP LPPM IPB), Jalan 
      Lodaya II/5 Bogor 16151, Indonesia.
AD  - Faculty of Veterinary Medicine, Bogor Agricultural University, Kampus Darmaga, 
      Bogor 16680, Indonesia.
LA  - eng
PT  - Journal Article
DEP - 20201015
PL  - Malaysia
TA  - Trop Life Sci Res
JT  - Tropical life sciences research
JID - 101539351
PMC - PMC7652245
OTO - NOTNLM
OT  - 3D Structure Model
OT  - Reverse Transcriptase
OT  - SRV-2 Indonesian Isolates
EDAT- 2020/11/21 06:00
MHDA- 2020/11/21 06:01
PMCR- 2020/10/01
CRDT- 2020/11/20 05:49
PHST- 2020/11/20 05:49 [entrez]
PHST- 2020/11/21 06:00 [pubmed]
PHST- 2020/11/21 06:01 [medline]
PHST- 2020/10/01 00:00 [pmc-release]
AID - tlsr-31-3-47 [pii]
AID - 10.21315/tlsr2020.31.3.4 [doi]
PST - ppublish
SO  - Trop Life Sci Res. 2020 Oct;31(3):47-61. doi: 10.21315/tlsr2020.31.3.4. Epub 2020 
      Oct 15.