Brand  (β version)

PDB ID: 5VBS

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Ligands
Code Name Style Show Link
Non-standard Residues
Code Name Show
93D (1r)-1,4-anhydro-2-deoxy-1-(2,4-diaminopyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol
DX [(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5VBS   PDBj   RCSB PDB   PDBe
Header : transferase/dna
Title : Structural basis for a six letter alphabet including GATCKX
Release Data : 2018-03-07
Compound :
mol_id molecule chains synonym
1 reverse transcriptase catalytic fragment A Pr180gag-pol
ec: 2.7.7.49,2.7.7.7
fragment: unp residues 683-987
mol_id molecule chains
2 DNA (5'-D(*CP*TP*TP*AP*TP*(DX)P*(DX)P*T)-3') B
mol_id molecule chains
3 DNA (5'-D(P*AP*(93D)P*(93D)P*AP*TP*AP*AP*G)-3') G
Source :
mol_id organism_scientific organism_common expression_system
1 Moloney murine leukemia virus (isolate Shinnick)  (taxid:928306) MoMLV Escherichia coli 'BL21-Gold(DE3)pLysS AG'  (taxid:866768)
strain: isolate Shinnick
gene: gag-pol
mol_id organism_scientific
2 Escherichia coli  (taxid:562)
synthetic: yes
mol_id organism_scientific
3 Escherichia coli  (taxid:562)
synthetic: yes
Authors : Singh, I., Georgiadis, M.M.
Keywords : Protein-DNA, AEGIS, unnatural base pair, host-guest system, transferase-dna complex
Exp. method : X-RAY DIFFRACTION ( 1.7490 Å )
Citation :

Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).

Singh, I.,Kim, M.J.,Molt, R.W.  et al.
(2017)  ACS Synth Biol  6 : 2118 - 2129

PubMed: 28752992
DOI: 10.1021/acssynbio.7b00150

Reaction

Chain : A
UniProt : P03355 (POL_MLVMS)
Reaction: EC: Evidence:
Physiological Direction:
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.49 PROSITE-ProRule:PRU00405
-
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 PROSITE-ProRule:PRU00405
-
Endonucleolytic cleavage to 5'-phosphomonoester. 3.1.26.4 PROSITE-ProRule:PRU00408
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000255 | PROSITE-ProRule:PRU00405
The RT polymerase active site binds 2 magnesium ions.
Mg(2+) ECO:0000250 | UniProtKB:Q2F7J3
ECO:0000269 | PubMed:16912289
Binds 2 Mn(2+)/Mg(2+) ions for ribonuclease H (RNase H) activity.
Mg(2+) ECO:0000305
Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.