Crystal structures of catalytic core domain of BIV integrase: implications for the interaction between integrase and target DNA

Yao, Xuemei; Fang, Shasha; Qiao, Wentao; Geng, Yi; Shen, Yuequan

doi:10.1007/s13238-010-0047-5

Cited by 3 publications

(5 citation statements)

References 35 publications

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“…The two catalytic domains interact with each other through the conserved, symmetric dimerization interface observed in most crystal structures of retroviral IN reported to date [2], [15], [16], [17], [18], [19], [20], [21], [22]. In contrast, the two CTDs dimerize through an asymmetric interface and are not related by a two-fold rotational symmetry.…”

Section: Resultsmentioning

confidence: 99%

“…Although many crystal structures are available for single or two-domain fragments of HIV [15], [16], [17], RSV [18], [19], [20], simian immunodeficiency virus [21], and bovine immunodeficiency virus IN [22], a three-domain retroviral IN complete with all structural domains has not been characterized using x-ray crystallography [3]. In this report, we describe crystallographic analyses of a three-domain RSV IN as well as its CCD-CTD fragment in a new crystal form at a much improved resolution compared to previous studies.…”

Section: Introductionmentioning

confidence: 99%

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A Possible Role for the Asymmetric C-Terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding

et al. 2013

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Integration of the retrovirus linear DNA genome into the host chromosome is an essential step in the viral replication cycle, and is catalyzed by the viral integrase (IN). Evidence suggests that IN functions as a dimer that cleaves a dinucleotide from the 3′ DNA blunt ends while a dimer of dimers (tetramer) promotes concerted integration of the two processed ends into opposite strands of a target DNA. However, it remains unclear why a dimer rather than a monomer of IN is required for the insertion of each recessed DNA end. To help address this question, we have analyzed crystal structures of the Rous sarcoma virus (RSV) IN mutants complete with all three structural domains as well as its two-domain fragment in a new crystal form at an improved resolution. Combined with earlier structural studies, our results suggest that the RSV IN dimer consists of highly flexible N-terminal domains and a rigid entity formed by the catalytic and C-terminal domains stabilized by the well-conserved catalytic domain dimerization interaction. Biochemical and mutational analyses confirm earlier observations that the catalytic and the C-terminal domains of an RSV IN dimer efficiently integrates one viral DNA end into target DNA. We also show that the asymmetric dimeric interaction between the two C-terminal domains is important for viral DNA binding and subsequent catalysis, including concerted integration. We propose that the asymmetric C-terminal domain dimer serves as a viral DNA binding surface for RSV IN.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Possible Role for the Asymmetric C-Terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding

et al. 2013

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“…Though important advances, these studies nonetheless fell short of achieving complete active site pictures because they lacked a critical component, the vDNA end substrate. Crystal structures of PFV (Réty et al, 2010; Valkov et al, 2009) and bovine immunodeficiency virus (BIV) (Yao et al, 2010) IN CCDs have been reported more recently (Table 1). …”

Section: The Start: Individual In Domain Structuresmentioning

confidence: 99%

“…Two codes are listed for studies that reported collective and minimized average NMR structures. f Ref, references: 1 – Dyda et al, 1994; 2 – Lodi et al, 1995; 3 – Bujacz et al, 1996; 4 – Cai et al, 1997; 5 – Cai et al, 1998; 6 – Goldgur et al, 1998; 7 – Maignan et al, 1998; 8 – Greenwald et al, 1999; 9 – Goldgur et al, 1999; 10 – Eijkelenboom et al, 1999; 11 – Chen, J.C. et al, 2000; 12 – Wang et al, 2001; 13 – Molteni et al, 2001; 14 – Cherepanov et al, 2005a; 15 – Christ et al, 2010; 16 – Wielens et al, 2010; 17 – Eijkelenboom et al, 2000; 18 – Hare et al, 2009b; 19 – Chen, Z. et al, 2000; 20 – Hare et al, 2000a; 21 – Yao et al, 2010; 22 – Bujacz et al, 1995; 23 – Bujacz et al, 1996; 24 – Bujacz et al, 1997; 25 – Lubkowski et al, 1998b; 26 – Lubkowski et al, 1998a; 27 – Lubkowski et al, 1999; 28 – Yang et al, 2000; 29 – Valkov et al, 2009; 30 – Réty et al, 2010; 31 – Hare et al, 2010a; 32 – Hare et al, 2010b; 33 – Maertens et al, 2010. …”

Section: Figmentioning

confidence: 99%

Structural biology of retroviral DNA integration

et al. 2011

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Three-dimensional macromolecular structures shed critical light on biological mechanism and facilitate development of small molecule inhibitors. Clinical success of raltegravir, a potent inhibitor of HIV-1 integrase, demonstrated the utility of this viral DNA recombinase as an antiviral target. A variety of partial integrase structures reported in the past 16 years have been instrumental and very informative to the field. Nonetheless, because integrase protein fragments are unable to functionally engage the viral DNA substrate critical for strand transfer inhibitor binding, the early structures did little to materially impact drug development efforts. However, recent results based on prototype foamy virus integrase have fully reversed this trend, as a number of X-ray crystal structures of active integrase-DNA complexes revealed key mechanistic details and moreover established the foundation of HIV-1 IN strand transfer inhibitor action. In this review we discuss the landmarks in the progress of IN structural biology during the past 17 years.

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“…It displays a significant interaction area, the values of which range from 1500–1300 Å 2 for HIV-1 and SIV to 750–700 Å 2 for RSV and PFV. A crystal form termed II of the CCD of BIV IN was found of particular interest, because it was observed that a dimer of canonical dimers (interaction area 1250 Å 2 ) was stabilized by a short interface named face-to-face (interaction area 580 Å 2 ), which could also occur during the formation of the IN-DNA complex [40] . Such face-to-face interface between canonical dimers is not observed in the structure of the PFV intasome [16] .…”

Section: Discussionmentioning

confidence: 99%

A Crystal Structure of the Catalytic Core Domain of an Avian Sarcoma and Leukemia Virus Integrase Suggests an Alternate Dimeric Assembly

et al. 2011

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Integrase (IN) is an important therapeutic target in the search for anti-Human Immunodeficiency Virus (HIV) inhibitors. This enzyme is composed of three domains and is hard to crystallize in its full form. First structural results on IN were obtained on the catalytic core domain (CCD) of the avian Rous and Sarcoma Virus strain Schmidt-Ruppin A (RSV-A) and on the CCD of HIV-1 IN. A ribonuclease-H like motif was revealed as well as a dimeric interface stabilized by two pairs of α-helices (α1/α5, α5/α1). These structural features have been validated in other structures of IN CCDs. We have determined the crystal structure of the Rous-associated virus type-1 (RAV-1) IN CCD to 1.8 Å resolution. RAV-1 IN shows a standard activity for integration and its CCD differs in sequence from that of RSV-A by a single accessible residue in position 182 (substitution A182T). Surprisingly, the CCD of RAV-1 IN associates itself with an unexpected dimeric interface characterized by three pairs of α-helices (α3/α5, α1/α1, α5/α3). A182 is not involved in this novel interface, which results from a rigid body rearrangement of the protein at its α1, α3, α5 surface. A new basic groove that is suitable for single-stranded nucleic acid binding is observed at the surface of the dimer. We have subsequently determined the structure of the mutant A182T of RAV-1 IN CCD and obtained a RSV-A IN CCD-like structure with two pairs of buried α-helices at the interface. Our results suggest that the CCD of avian INs can dimerize in more than one state. Such flexibility can further explain the multifunctionality of retroviral INs, which beside integration of dsDNA are implicated in different steps of the retroviral cycle in presence of viral ssRNA.

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Crystal structures of catalytic core domain of BIV integrase: implications for the interaction between integrase and target DNA

Cited by 3 publications

References 35 publications

A Possible Role for the Asymmetric C-Terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding

A Possible Role for the Asymmetric C-Terminal Domain Dimer of Rous Sarcoma Virus Integrase in Viral DNA Binding

Structural biology of retroviral DNA integration

A Crystal Structure of the Catalytic Core Domain of an Avian Sarcoma and Leukemia Virus Integrase Suggests an Alternate Dimeric Assembly

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