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Annotation rule MF_04144
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General rule information [?]

Accession MF_04144
Dates 20-DEC-2019 (Created)
3-FEB-2020 (Last updated, Version 3)
Name TERL_LAMBDA
Scope
Viruses; Caudovirales
Template P03708 (TERL_LAMBD)

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
TERL
case <FTTag:Magnesium>
Protein name
RecName: Full=Terminase, large subunit;
AltName: Full=DNA-packaging protein;
AltName: Full=Large terminase protein;
Includes:
RecName: Full=Endonuclease;
EC 3.1.21.4;
Includes:
RecName: Full=Helicase;
EC 3.6.4.12;
Includes:
RecName: Full=ATPase;
EC 3.6.4.-;
else
Protein name
RecName: Full=Terminase, large subunit;
AltName: Full=DNA-packaging protein;
AltName: Full=Large terminase protein;
Includes:
RecName: Full=Helicase;
EC 3.6.4.12;
Includes:
RecName: Full=ATPase;
EC 3.6.4.-;
end case

Comments [?]

case <OC:Lambdavirus>
Function The terminase large subunit acts as an ATP driven molecular motor necessary for viral DNA translocation into empty capsids and as an endonuclease that cuts the viral genome from the concetamer to initiate and to end the packaging reaction. The terminase lies at a unique vertex of the procapsid and is composed of two subunits, a small terminase subunit involved in viral DNA recognition (binding to packaging sequence cos), and a large terminase subunit possessing endonucleolytic, ATPase and helicase activities (DNA maturation and packaging). The terminase binds cooperatively with the host factor IHFA/IHFB to the cos site at the junction of adjacent viral genomes. The endonuclease activity cleaves the viral DNA generating 5'overhangs of 12 bp in length. The helicase activity separates the cohesive ends generating the single-stranded 'sticky' ends of the mature genome. IHFA/IHFB is also necessary for the strand separation activity of the terminase. The terminase remains bound to the left end of the genome to be packaged, forming a stable DNA-terminase complex. In a reaction facilitated by the viral assembly catalyst gpFI, the DNA-terminase complex binds to the portal of the procapsid thereby activating the translocase activity of the terminase. The terminase packages the viral DNA into the procapsid until the next cos site on the concatemer reaches the complex. The downstream cos site is then cut generating the mature right end of the genome, the heterotrimer undocks from the DNA-filled head and remains bound to the left end of concatemer's next genome.
Subunit Heterotrimer of two small and one large terminase subunits. The catalytically competent terminase is composed of a tetramer of heterotrimers. The tetramer forms a ring structure large enough to encircle duplex DNA. Host IHFA/IHFB induces bending of viral DNA to facilitate the assembly of the terminase tetramer of heterotrimers. Interacts (via N-terminus) with the terminase small subunit (via C-terminus). Interacts (via C-terminus) with the portal protein; this interaction allows the packaging of viral DNA.
Domain The N-terminus is involved in the formation of the heterotrimer with the small subunit. The N-terminus part contains the translocase activity involved in DNA packaging. At the N-terminus, there is a high affinity ATPase center that is probably needed for the packaging activity. The Walker A motif of the ATPase center is responsible for interacting with the ATP phosphate and the Q motif governs force generation and the interaction with DNA. The C-terminus contains the site specific endonuclease (cos-cleavage) and strand separation (helicase) activities required for genome maturation. A second ATPase catalytic site regulates the genome maturation. The C-terminus very end is involved in binding to the procapsid. Contains a basic leucine zipper (bZIP) that may be involved in the formation of the terminase.
else
Function The terminase large subunit acts as an ATP driven molecular motor necessary for viral DNA translocation into empty capsids and as an endonuclease that cuts the viral genome from the concetamer to initiate and to end the packaging reaction. The terminase lies at a unique vertex of the procapsid and is composed of two subunits, a small terminase subunit involved in viral DNA recognition, and a large terminase subunit possessing endonucleolytic, ATPase and helicase activities (DNA maturation and packaging). The endonuclease activity cleaves the viral DNA generating 5'overhangs. The helicase activity separates the cohesive ends generating the single-stranded 'sticky' ends of the mature genome. The DNA-terminase complex binds to the portal of the procapsid thereby activating the translocase activity of the terminase. The terminase packages the viral DNA into the procapsid until the next concatemer reaches the complex. The downstream site is then cut generating the mature right end of the genome, the heterotrimer undocks from the DNA-filled head and remains bound to the left end of concatemer's next genome.
Subunit Interacts (via N-terminus) with the terminase small subunit (via C-terminus); the active complex is probably heterooligomeric. Interacts (via C-terminus) with the portal protein; this interaction allows the packaging of viral DNA.
Domain The N-terminus is involved in the formation of the heterotrimer with the small subunit. The N-terminus part contains the translocase activity involved in DNA packaging. At the N-terminus, there is a high affinity ATPase center that is probably needed for the packaging activity. The Walker A motif of the ATPase center is responsible for interacting with the ATP phosphate and the Q motif governs force generation and the interaction with DNA. The C-terminus contains the site specific endonuclease (cos-cleavage) and strand separation (helicase) activities required for genome maturation. A second ATPase catalytic site regulates the genome maturation. The C-terminus very end is involved in binding to the procapsid. Contains a basic leucine zipper (bZIP) that may be involved in the formation of the terminase.
end case
case <FTTag:Magnesium>
Cofactor Mg(2+)
Catalytic activity Reaction=Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.; EC=3.1.21.4;
end case
Catalytic activity RHEA:13065: ATP + H2O = ADP + H(+) + phosphate
Subcellular location Host cytoplasm. Note=The terminase lies at a unique vertex of the procapsid during viral DNA packaging.
Similarity Belongs to the lambdavirus large terminase family.

Keywords [?]

case <FTTag:Magnesium>
end case

Gene Ontology [?]

GO:0098009; Cellular component: viral terminase, large subunit.
GO:0005524; Molecular function: ATP binding.
GO:0016887; Molecular function: ATPase activity.
GO:0003678; Molecular function: DNA helicase activity.
GO:0004519; Molecular function: endonuclease activity.
GO:0019073; Biological process: viral DNA genome packaging.
GO:0009036; Molecular function: type II site-specific deoxyribonuclease activity.
case <FTTag:Magnesium>
GO:0046872; Molecular function: metal ion binding.
end case

Cross-references [?]

Pfam PF05876; Terminase_GpA; 1;

Features [?]

case <OC:Lambdavirus>
From: TERL_LAMBD (P03708)
Key     From     To       Description   Tag   Condition   FTGroup
REGION     1     48       Interaction with the terminase small subunit        
REGION     166     349       DNA packaging/ATPase        
REGION     401     586       Endonuclease/helicase        
REGION     610     641       Prohead binding        
end case
REGION (Optional)     491     498       ATP-binding     G-x(4)-G-K-P  
REGION (Optional)     588     616       Leucine zipper     L-x(6)-L-x(6)-[IL]-x(6)-L-x(6)-L  
MOTIF     76     83       Walker A motif     x(3)-[QR]-x-[GLM]-[FKILY]-[ST]   1
MOTIF     174     179       Walker B motif     x(4)-D-E   1
ACT_SITE     179     179       For ATPase activity     E  
METAL     401     401       Magnesium; catalytic; for nuclease activity   Magnesium   D  
SITE     46     46       ATP-binding     Y  

Additional information [?]

Size range 540-720 amino acids
Related rules None
Fusion None