HERV-K 5q33.3 provirus ancestral pol protein; HERV-K10 pol protein; HERV-K107 pol protein (includes: reverse transcriptase; RT, ribonuclease H; Rnase H, integrase; IN)

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Function

early post-infection, reverse transcriptase converts the viral RNA genome into double-stranded viral DNA
Rnase H domain of the reverse transcriptase performs two functions
- it degrades the RNA template & specifically removes the RNA primer from the RNA/DNA hybrid
- following nuclear import, the integrase catalyzes the insertion of the linear, double-stranded viral DNA into the host cell chromosome
endogenous pol proteins may have kept, lost or modified their original function during evolution

the LPQG & YXDD motifs are catalytically important & conserved among many retroviruses
belongs to the beta type-B retroviral polymerase family, HERV class-II K(HML-2) subfamily
contains 1 integrase catalytic domain
contains 1 integrase-type DNA-binding domain
contains 1 integrase-type Zn+2 finger
contains 1 reverse transcriptase domain
contains 1 Rnase H domain

HERV-K 5q33.3 has a type 1 genome
the HERV-K(HML-2) family contains type 1 & type 2 genomes depending on the absence or presence of 292 nucleotides at the 5'-end of the env gene
type 1 genomes lack a pol stop codon, leading to expression of a fusion protein containing a portion of the Env sequence

this protein is synthesized as Gag-Pro & Gag-Pro-pol polyprotein precursor
by similarity with type-B retroviruses, thought to be generated by -1 frameshifts occurring at the Gag-Pro & Pro-pol genes boundaries