reverse transcription of viral rna into double - stranded ( ds ) dna , and the subsequent insertion of the synthesized viral dna ( vdna ) into a host chromosome , are characteristic features of retroviruses including human immunodeficiency virus type 1 ( hiv-1 ) . the reverse transcription and integration of the viral genome is sequentially catalyzed by the enzymes reverse transcriptase ( rt ) and integrase ( in ) , respectively . these retroviral enzymes are originally packaged in the viral particle along with the viral genomic rna . after synthesis of vdna by rt , in acts on the termini of vdna and catalyzes insertion of the vdna into the host chromosome through two sequential enzymatic reactions : 3-end processing and strand - transfer ( katz and skalka , 1994 ) . currently , a clinically approved in inhibitor specifically targets strand - transfer activity but not 3-end processing activity ( summa et al . , 2008 ) . therefore , the in inhibitor is referred to as a strand - transfer inhibitor ( sti ) . the sti shows very potent antiviral activity ; however , emergence of sti - resistant variants is inevitable ( metifiot et al . , 2010 ) , as seen in patients treated with a combination of inhibitors against rt and protease activities . efforts to develop novel drugs with distinct inhibitory mechanisms must continue so that we can effectively treat hiv-1 infections . for development of novel in inhibitors , in addition to its enzymatic action , other non - enzymatic functions of in , as described below , might be the next target(s ) ( luo and muesing , 2010 ) . human immunodeficiency virus type 1 in is composed of 288 amino acids with three structurally distinct domains ( li et al . , 2011 ) : an n - terminal domain ( ntd ) , a central catalytic core domain ( ccd ) , and a c - terminal domain ( ctd ; figure 1 ) . the ntd contains a highly conserved ( his - his - cys - cys , hhcc ) motif , which binds to zinc ions ( zn ) and folds a helix - turn - helix ( hth ) structure . through a tetrahedral attachment to the hhcc motif , zn enhances both multimerization and enzymatic activities of hiv-1 in in vitro ( burke et al . , 1992 ; the ccd contains the highly conserved asp , asp , and glu ( dde ) residues directly involved in the catalytic activities of in ( engelman and craigie , 1992 ; kulkosky et al . , 1992 ; lafemina et al . , 1992 ; bushman et al . , overall topology of the ccd is similar to those of ribonuclease h ( rnaseh ) , the holliday junction resolvase ruvc , and bacteriophage transposase mu . despite lack of sequence similarity between the ccd and rnaseh , there is remarkable similarity in the positioning of the two asp catalytic residues ( dyda et al . , 1994 ) . the ctd , consisting of a structure that closely resembles src homology 3 domains ( sh3-like ) , possesses sequence- and metal ion - independent dna binding activity ( eijkelenboom et al . , 1995 ; lodi et al . , 1995 ) . each domain has been demonstrated to form a dimer and higher multimerization states ( dyda et al . , 1994 ; eijkelenboom et al . , 1995 ; cai et al . , hiv-1 in is encoded by the pol region and composed of 288 amino acids with three structurally distinct domains : an n - terminal domain ( ntd ) ; a central catalytic core domain ( ccd ) ; and a c - terminal domain ( ctd ) . the ccd contains the highly conserved dde motif , which is directly involved in the catalytic activities of in . overall topology of the ccd is similar to that of ribonuclease h ( rnaseh ) . the ntd , contains a highly conserved hhcc motif , which binds to zinc and folds a helix - turn - helix ( hth ) structure . the ctd , consisting of a structure that closely resembles src homology 3 domains ( sh3 ) , possesses sequence- and metal ion - independent dna binding activity . recently , the entire prototype foamy virus ( pfv ) in in a complex with its cognate vdna ends , referred to as the intasome , has been successfully crystallized ( hare et al . , 2010 ) . the crystal structure analysis of the pfv intasome revealed an unprecedented tetramer structure for in ( see cherepanov et al . the in tetramer structure observed in the pfv intasome demonstrated that two sets of in dimer acts on each vdna end ( figure 2 ) . the outer subunits of each in dimer might be speculated to have supportive or other functions , such as engagement of target dna or interaction with host factors . several models for the in tetramer have been proposed from previous structure analysis using partial in fragments possessing the ntd  ccd or ccd  ctd ( chen et al . , 2000 ; wang et al . , 2001 ; hare et al . , 2009a ) . however , these in tetramer models are different from those observed in the active pfv intasome ( craigie , 2010 ) . stable interaction of in with 3-end processed vdna in the intasome might be a plausible explanation for the difference . the stable in tetramer formation observed in the intasome reflects the in - dna complex required for proper concerted integration of both vdna ends into the proximal sites of the target host chromosomal dna . furthermore , analysis of the pfv intasome interacting with the sti elucidated its inhibitory mechanism . based on the pfv intasome structure as a template , structural modeling of the hiv-1 intasome structural analysis of this intasome revealed numerous details of retroviral integration and will contribute to the design of the next generation of hiv-1 in catalytic inhibitors . the functional significance of the dna - independent in tetramer as observed by analysis of partial in fragments ( chen et al . , 2000 ; wang et al . , 2001 ; after entry into cells , retroviral genomic rna ( vrna ) is reverse transcribed into dna ( vdna ) by rt . then , vdna is transported into the nucleus ( nuclear import ) and finally integrated into host chromosomal dna ( black lines ) . in forms a functional tetramer with vdna ends ( intasome ) to assist with integration . subsequent repair processes by host dna repair machinery establishes the proviral dna , in which retrovirus dna is stably integrated into host chromosomal dna . in tetramer structures for its enzymatic ( integration ) and non - enzymatic functions ( reverse transcription and nuclear import ) and possible involvement of host factors the vrna , vdna , and host dna are shown as blue , red , and black lines , respectively . originally , we found that introduction of amino acid substitutions at conserved hhcc residues in the ntd of hiv-1 in resulted in almost complete abrogation of proviral dna formation , concomitant with a severe reduction in vdna synthesis . this suggests the mutations in the in affected the viral life cycle at steps prior to integration ( masuda et al . , 1995 ) . further genetic analysis of hiv-1 in revealed that the pleiotropic effects of in mutations affected uncoating ( masuda et al . , 1995 ; leavitt et al . , 1996 ; nakamura et al . , 1997 ; briones et al . , 2010 ) , reverse transcription ( engelman et al . , 1995 ; masuda et al . , 1995 ; wu et al . , 1999 ; tsurutani et al . , 2000 , 1997 ; tsurutani et al . , 2000 ; ikeda et al . , 2004 ) , and protein processing during viral particle assembly and maturation ( mohammed et al . , 2011 ) . importantly , hiv-1 carrying point mutations at the catalytic sites of in ( dde ) affected the integration step , but not vdna synthesis ( masuda et al . , 1995 ) . thus , the pleiotropic effects of in mutations might not be directly related to the loss of its catalytic function . these experiments suggest that in may possess non - enzymatic roles throughout the viral replication cycle ( figure 2 ) . among the possible non - enzymatic roles of in , there has been an accumulation of evidence to suggest involvement of retroviral in during reverse transcription ( engelman et al . , 1995 ; the contribution of in during reverse transcription has also been noticed in a retrovirus - like element of saccharomyces cerevisiae , ty3 ( nymark - mcmahon and sandmeyer , 1999 ; nymark - mcmahon et al . , 2002 ) . a previous study from our laboratory showed that reverse transcription of hiv-1 was abrogated by knocking down a host factor , survival motor neuron ( smn)-interacting protein 1 ( sip1/gemin2 ) , which binds to hiv-1 in ( hamamoto et al . , 2006 ) . gemin 2 is a component of the smn complex that mediates the assembly of spliceosomal small nuclear ribonucleoproteins and nucleolar ribonucleoproteins ( fischer et al . , 1997 ; liu et al . , 1997 ; buhler et al . , 1999 ; jablonka et al . , 2001 ; meister et al . , 2001 ) . in a subsequent study , we demonstrated that hiv-1 in and gemin2 synergistically stimulate rt activity by enhancing the assembly of rt on viral rna in vitro ( nishitsuji et al . , 2009 ) . chow and colleagues have also reported that hiv-1 in stimulates rt activity through physical interactions with rt ( zhu et al . , 2004 ) . thus , in might possess a direct function to support efficient reverse transcription by rt . delineation of the in mutant structure could provide clues for depicting the in conformation required for non - enzymatic functions . nuclear magnetic resonance ( nmr ) analysis of an isolated ntd has shown that the ntd exists in two conformational states , the e and d forms ( cai et al . , 1997 ) . a previous study using nmr spectroscopy indicated that the ntd mutant protein , in which the tyr 15 residue was replaced with ala ( y15a ) , folds correctly but only as the e form ( nomura et al . , 2006 ) . the in tetramer structure was formed through interaction of ntd  ccd between the inner subunits in the intasome ( hare et al . , 2010 ) . the residues 1326 and 4045 in the ntd interact extensively with residues 150196 in the ccd of the other subunit . ccd interaction to form the in tetramer has been proposed from previous crystal structure analysis using the ntd  ccd in fragments ( wang et al . , 2001 ; hare et al . , 2009b ) . as observed in these previous analyses , the hydrogen - bond contacts between the side chains of ccd residues gln164 and arg187 and the backbones of the ntd residues lys14 and tyr15 also persist in the recent structure - based model of the hiv-1 in intasome ( krishnan et al . , 2010 ) . hiv-1 carrying in mutations at the lys186 , arg187 , and lys188 residues exhibited a reverse transcription - defective phenotype ( tsurutani et al . , 2000 ) as found in the ntd mutants including y15a . these experimental data suggest that the functional tetramer form , stabilized with the ntd  ccd interaction , might be critical for the non - enzymatic function of in during reverse transcription . numerous host factors that interact with hiv-1 in have been reported ( al - mawsawi and neamati , 2007 ) . the best characterized factor is lens epithelium - derived growth factor / transcription co - activator p75 ( ledgf / p75 ; cherepanov et al . , 2003 ) for chromosomal targeting of hiv-1 in ( maertens et al . , 2003 , 2004 ; the crystal structure analysis of the pfv intasome ( hare et al . , 2010 ) together with results from previous studies ( li et al . , 2006 ; hare et al . , 2009a ) suggest that synapsis formation with dna ends of the virus through tetramerization of in might be critical for proper assembly and/or a stable and functionally active intasome . importantly , ledgf / p75 stabilizes the functional tetramer of in for its enzymatic function . meanwhile , a reduction of the tetramer form of in was reproduced when wild - type in was expressed in cells in which endogenous gemin2 was knocked down by rna interference ( nishitsuji et al . , 2009 ) . we also noticed that the intracellular stability and multimer formation of in , especially the tetramer formation of in , were dramatically reduced by in mutations that led to a reverse transcription - defective phenotype . thus , in the absence of vdna , host factors might be involved in forming or maintaining highly ordered structures of in , which is critical for non - enzymatic function . therefore , inhibition of the interaction between in and host factors could be a novel therapeutic approach for the design and development of new classes of in inhibitors targeting non - enzymatic functions . it is obvious that in must be closely associated with the viral genome complex to form an active intasome upon the completion of reverse transcription . physical interaction of in with rt ( zhu et al . , 2004 ; wilkinson et al . , 2009 ) how is the in structure in the absence of vdna before and during reverse transcription maintained ? what is the contribution of host factors to in conformation that is required for non - enzymatic functions ? the highly ordered in structure and/or its interface structure for interaction with host factors required for non - enzymatic in function(s ) should be determined . finally , it should be emphasized that in mutations affecting non - enzymatic function resulted in severe deleterious affects to hiv-1 replication compared with in mutations that specifically affected catalytic activity . clinical efficacy of the sti that blocks in catalytic activity guarantees that a greater impact on hiv-1 control would be achieved with a novel inhibitor that blocks the non - enzymatic function of in . the author declares that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest .