Reverse transcriptase

2010-12-26T16:30:54Z

Brian Foley: Corrected minor typo in Structure section.

[[Image:1hmv1.png|left|200px|thumb|Crystal Structure of unliganded HIV-1 Reverse transcriptase, [[1hmv]]]]
{{STRUCTURE_1hmv| PDB=1hmv | SIZE=300| SCENE=Reverse_transcriptase/Cv/1 |right|CAPTION=HIV-1 Reverse transcriptase, [[1hmv]] }}

[[Reverse transcriptase]] (RT) or RNA-dependent DNA polymerase transcribes single-stranded RNA into double-stranded [[DNA]]. HIV-1 RT is from the human immunodeficiency virus and is a heterodimer of P66 and P51. The images at the left and at the right correspond to one representative RT structure, ''i.e.'' crystal structure of HIV-1 Reverse transcriptase ([[1hmv]]). P15 is its RNAse H domain. NNRTI are the non-nucleoside inhibitors of HIV-1 RT. M-MLV is RT from the leukemia virus. Being the protein that gives their name to Retroviruses, Reverse Transcriptase is, in company of [[Hiv protease|Protease]] and [[Hiv integrase|Integrase]], the most important part of the protein system involved in the process of infection of viruses like HIV, MuLV and AMV, and has the unusual property of transcribing ssRNA into dsDNA going against the Central Dogma of Molecular Biology.
Since its discovery in 1970, the study of its properties and mechanisms of action have been of high interest among the scientific community due to the unique properties that makes it an important medical target enzyme and important tool for genetic engineering applications like RT-PCR in the construction of cDNA libraries.

Reverse Transcriptase is one of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground]. <scene name='Reverse_transcriptase/Presentation/3' caption='The hand-like two-enzymes-in-one protein that amazingly makes DNA from RNA'>-- CBI Molecular Playground Model --</scene>

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==Structure==

<applet size='[450,338]' frame='true' align='right' name='Reverse Transcriptase scene='Reverse_transcriptase/Presentation/3' caption='The hand-like two-enzymes-in-one protein that amazingly makes DNA from RNA' />
This ''hand-like'' <scene name='Reverse_transcriptase/Chains/2'>heterodimer</scene> protein that has an usual length of 1000 residues (560 in Chain A and 440 for B), the third of them involved in alpha helical and almost a quarter in beta sheets, showing α+β <scene name='Reverse_transcriptase/Secondary/2'>secondary structure</scene> domains; <scene name='Reverse_transcriptase/Chaina/2'>Chain A</scene> has an usual weight of 66KDa whereas <scene name='Reverse_transcriptase/Chainb/2'>Chain B</scene> is around 51KDa, those monomers are derived from the same gene but p51 lacks the amino acids of one active site and has a different tertiary structure conformation compared with p66, for this reason is enzymatically inactive. <ref>PMID: 1377403</ref> 
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==Function==

{{STRUCTURE_3hvt| PDB=3jyt | SCENE='Reverse_transcriptase/Initial/1' size='[450,338]' align='right' frame='true' caption='Reverse Transcriptase' }}
As a RNA-dependent DNA Polymerase, is able to recognize the initial RNA, transcribe it to ssDNA, cleave the remaining RNA and then build up the dsDNA, to do this the protein has two active catalytic zones. Chain A has the <scene name='Reverse_transcriptase/Fingers/4'>Polymerase active site</scene> that consist of two ''finger-like'' domains, one of them recognizes the initial nucleic acid by h-bonds interactions with phosphate groups of the side chains, then both domains make a conformational change closing the recognition hole to allow the second domain with the support a <scene name='Reverse_transcriptase/Magnesium/2'>Magnesium ion</scene> coordination system, begin the transcription process adding the specific DNA nucleotides; this change is allowed by a <scene name='Reverse_transcriptase/Flexible/2'>flexible zone</scene> between the two previous domains that is used as a common pharmaceutical target site in order to prevent this change and by this way inhibit the activity, but this one is the only zone of the Chain A that has non-conserved aminoacids giving the virus more drug resistance. [http://consurfdb.tau.ac.il/chain_selection.php?pdb_ID=1JLB]
As the same rate that the polymerization process occurs, the other active site known as the <scene name='Reverse_transcriptase/Rnase/2'>Ribonuclease H domain</scene>, cleaves the RNA releasing the ssDNA that comes again trough the Polymerase active site to become dsDNA (all this with a <scene name='Reverse_transcriptase/Magnesium2/2'>second Magnesium</scene> coordinative system, that allows non-specific recognition, just with phosphates). Finally Chain B despite of the similar aminoacid sequence with Chain A has no enzyme activity, possibly its function is to stabilize and communicate both active sites, this varying the length between them in order to synchronize both functions.
This seems to be the most general idea of the mechanism of action of Reverse Transcriptase, however the process remains unclear and new approaches are being reported. [http://www.nature.com/nature/journal/v453/n7192/full/nature06941.html]

One of the principal issues about this protein comparative with the usual DNA polymerase (besides to the similarity with the Klenow fragment), is the lack of a correction mechanism (usually made by DNA PolIII in the [[User:Karl E. Zahn/RB69 DNA polymerase (GP43)|DNA Polymerase]]) that increase the quota of errors, producing more mutations and by this way giving more facultative and resistance abilities to the virus.
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== 3D Structures of Reverse transcriptase ==

=== HIV-1 RT ===

[[3dlk]], [[1hmv]] - P66/P51 
[[1mu2]], [[1jle]], [[1hpz]], [[1hqu]], [[1qe1]], [[1dlo]] - P66/P51 (mutant) 
[[1har]] - P66 N-terminal 
[[3lp0]], [[3lp1]], [[3lp2]], [[1vrt]] - P66/P51+NNRTI nevirapine 
[[2hnd]], [[2hny]], [[1s1u]], [[1s1x]], [[1lw0]], [[1lwc]], [[1lwe]], [[1lwf]], [[1jlb]], [[1jlf]], [[1fkp]] - P66/P51 (mutant)+NNRTI nevirapine 
[[3m8p]], [[3mec]] - P66/P51+NNRTI etravirine 
[[3med]] - P66/P51 (mutant)+NNRTI etravirine 
[[3mee]], [[2zd1]]- P66/P51+NNRTI rilpivirine 
[[3meg]], [[2ze2]], [[3bgr]] - P66/P51 (mutant)+NNRTI rilpivirine 
[[1ikw]], [[1fk9]] - P66/P51 +NNRTI efavirenz 
[[1jkh]], [[1ikv]], [[1fko]] - P66/P51 (mutant)+NNRTI efavirenz 
[[3dya]], [[3e01]], [[3drp]] - P66/P51+NNRTI pyrazole 
[[3drr]], [[3drs]] - P66/P51 (mutant)+NNRTI pyrazole 
[[3irx]], [[3is9]], [[3lak]], [[3lal]], [[3lam]], [[3lan]], [[3ffi]], [[3di6]], [[3dle]], [[3dlg]], [[2rki]], [[3c6t]], [[3c6u]], [[2rf2]], [[2vg5]], [[2vg6]], [[2vg7]], [[2opp]], [[1jlq]], [[1ep4]], [[1c0t]], [[1c0u]], [[1dtt]], [[1dtq]], [[1bqm]], [[1rt1]], [[1rt2]], [[1rev]], [[1rtj]], [[1vru]], [[1hnv]], [[1hni]] - P66/P51+NNRTI 
[[1s1t]], [[1s1v]], [[1s1w]], [[1s6p]], [[1s6q]], [[1s9e]], [[1s9g]], [[1suq]], [[1sv5]], [[3dm2]], [[3dmj]], [[3dok]], [[3dol]], [[2opq]], [[2opr]], [[2ops]], [[2ic3]], [[2hnz]], [[1jlg]], [[1bqn]], [[1uwb]], [[1tvr]] - P66/P51 (mutant)+NNRTI 
[[3kk1]], [[1c1b]], [[1rti]] - P66/P51+nucleotide inhibitor 
[[1jla]] - P66/P51 (mutant)+ nucleotide inhibitor 
[[3ig1]] - P66/P51+ inhibitor beta-thujaplicinol 
[[3i0r]], [[3i0s]], [[3m8q]], [[3isn]], [[3ith]], [[1c1c]] - P66/P51+ pyrimidine derivative 
[[1ikx]] - P66/P51 (mutant)+ pyrimidine derivative 
[[1tv6]] - P66/P51+ pyridine derivative 
[[1jlc]], [[1iky]], [[1eet]] - P66/P51(mutant)+ pyridine derivative 
[[2b5j]], [[2ban]], [[2be2]], [[1rth]], [[1hvt]] - P66/P51+ pyridone derivative 
[[1lw2]], [[1rt3]] - P66/P51 (mutant)+ pyridone derivative 
[[1tkt]], [[1tkx]], [[1tkz]], [[1tl1]], [[1tl3]] - P66/P51+ quinoline derivative 
[[2b6a]] - P66/P51+ THR-50 
[[2i5j]] - P66/P51 (mutant)+hydrazone derivative 
[[1rt4]], [[1rt5]], [[1rt6]], [[1rt7]] - P66/P51+ carboxanilide derivative 
[[1klm]] - P66/P51+piperazine derivative 
[[2jle]] – P66+NNRTI 
[[3kjv]], [[3kk3]], [[1r0a]], [[1n5y]], [[1n6q]], [[1hys]] - P66/P51+DNA 
[[1j5o]], [[1rtd]] - P66/P51 (mutant)+DNA 
[[1hvu]] - P66/P51+RNA 
[[1t03]], [[1t05]] - P66/P51+DNA+Fab+tenofovir 
[[2hmi]] - P66/P51 (mutant)+DNA+Fab 
[[2iaj]] - P66/P51 (mutant)+ATP 
[[3kk2]] - P66/P51+DNA+ATP 
[[3jyt]] - P66/P51 (mutant)+DNA+ATP 
[[1rdh]], [[1hrh]] – P15 
[[3lp3]] – P15+inhibitor MK3 
[[3k2p]] – P15+inhibitor beta-thujaplicinol 
[[3hyf]] – P15+pyrimidine derivative 
[[1o1w]] – P15+Mg - NMR 

=== M-MLV ===

[[2hb5]], [[1mml]] - catalytic fragment 
[[2r2r]], [[2r2t]], [[2fjv]], [[2fjw]] – catalytic fragment+DNA 
[[2r2s]], [[2r2u]] - catalytic fragment+DNA+Co Bleomycin 
[[2fjx]], [[1ztw]] - catalytic fragment+DNA 
[[1ztt]] - catalytic fragment+DNA+netropsin 
[[1rw3]], [[1nnd]] – fragment (mutant) 
[[1i6j]], [[1d0e]], [[1d1u]], [[1qaj]], [[1qai]] – N-terminal+DNA 

==See Also==

* Reverse Transcriptase at [http://en.wikipedia.org/wiki/Reverse_transcriptase Wikipedia]
* Molecule of the Month (09/2002) at [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb33_1.html RCSB Protein Data Bank]
* List of Reverse Transcriptase articles at [http://www.proteopedia.org/wiki/index.php/Category:Reverse_transcriptase Proteopedia] and at [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb33_report.html RCSB Protein Data Bank]
* Model of Reverse Transcriptase as one of the [[CBI Molecules|CBI Molecules]] on the [http://www.molecularplayground.org Molecular Playground]
* See [[Transcription]] for additional Proteopedia articles on the subject.
* For additional information, see: [[Human Immunodeficiency Virus]]
* For additional information, see: [[Transcription and RNA Processing]]
 
==References==
<references />
*[2] Consurf Server Data Base. Evolutionary conservation profile for Reverse Transcriptase PDB file 1JLB 
*[3] Abbondanzieri, E.A. ''et al''. Nature 453, 184-189 (2008) | [http://dx.doi.org/10.1038/nature06941 doi:10.1038/nature06941]

[[Category:Topic Page]]

Talk:Reverse transcriptase

2010-12-23T16:40:09Z

Brian Foley: added first comment. on An tutorial for HIV RT.

David Marcey (who is a [http://www.proteopedia.org/wiki/index.php/User:David_Marcey member here] at protopedia) has a nice [http://www.callutheran.edu/BioDev/omm/jmol/hivrt/hivrt.html tutorial of HIV-1 reverser transcriptase], done in JMOL, at his [http://www.callutheran.edu/BioDev/omm/exhibits.htm online macromolecular museum].

It would be nice to provide a link to that, at the very least. I'd like to learn more about what Protopedia hopes to do for each molecule/structure.

User:Brian Foley

2008-08-15T15:51:04Z

Brian Foley:

PhD from University of Vermont 1995 Molecular Genetics

HIV Epidemiology research 1995 - present LANL HIV Databases

Proteopedia - User contributions [en]

Reverse transcriptase

Talk:Reverse transcriptase

User:Brian Foley