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HAMAP rule MF_04144

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General rule information [?]

Accession MF_04144
Dates 20-DEC-2019 (Created)
19-NOV-2022 (Last updated, Version 9)
Name TERL_LAMBDA
Scope(s) Viruses
Caudoviricetes
Template(s) P03708 (TERL_LAMBD); [ Recover all ]
Triggered by HAMAP; MF_04144 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier TERL
case <FTTag:Magnesium>
RecName: Full=Terminase, large subunit;<br /> AltName: Full=DNA-packaging protein;<br /> AltName: Full=Large terminase protein;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Includes:<br /> RecName: Full=Endonuclease;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EC=<a href="https://enzyme.expasy.org/EC/3.1.21.4">3.1.21.4</a>;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Includes:<br /> RecName: Full=Helicase;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EC=<a href="https://enzyme.expasy.org/EC/3.6.4.12">3.6.4.12</a>;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Includes:<br /> RecName: Full=ATPase;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EC=<a href="https://enzyme.expasy.org/EC/3.6.4.-">3.6.4.-</a>;
else
RecName: Full=Terminase, large subunit;<br /> AltName: Full=DNA-packaging protein;<br /> AltName: Full=Large terminase protein;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Includes:<br /> RecName: Full=Helicase;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EC=<a href="https://enzyme.expasy.org/EC/3.6.4.12">3.6.4.12</a>;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Includes:<br /> RecName: Full=ATPase;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EC=<a href="https://enzyme.expasy.org/EC/3.6.4.-">3.6.4.-</a>;
end case

Comments [?]

case <OC:Lambdavirus>
FUNCTIONThe 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.
SUBUNITHeterotrimer 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.
DOMAINThe 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
FUNCTIONThe 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.
SUBUNITInteracts (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.
DOMAINThe 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 Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
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 Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216;
SUBCELLULAR LOCATIONHost cytoplasm. Note=The terminase lies at a unique vertex of the procapsid during viral DNA packaging.
SIMILARITYBelongs to the lambdavirus large terminase family.

Keywords [?]

ATP-binding
Endonuclease
Host cytoplasm
Hydrolase
Nuclease
Nucleotide-binding
Viral genome packaging
Viral release from host cell
case <FTTag:Magnesium>
Magnesium
Metal-binding
end case

Gene Ontology [?]

GO:0098009; Cellular component:viral terminase, large subunit
GO:0005524; Molecular function:ATP binding
GO:0016887; Molecular function:ATP hydrolysis 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 [?]

From: TERL_LAMBD (P03708)
Key From To Description Tag Condition FTGroup
case <OC:Lambdavirus>
REGION 1 48 /note="Interaction with the terminase small subunit"
REGION 166 349 /note="DNA packaging/ATPase"
REGION 401 586 /note="Endonuclease/helicase"
/note="Endonuclease/helicase"
REGION 610 641 /note="Prohead binding"
end case
BINDING 491 498 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 G-x(4)-G-K-P
REGION 588 616 /note="Leucine zipper" L-x(6)-L-x(6)-[IL]-x(6)-L-x(6)-L
MOTIF 76 83 /note="Walker A motif" x(3)-[QR]-x-[GLM]-[FKILY]-[ST] 1
MOTIF 174 179 /note="Walker B motif" x(4)-D-E 1
ACT_SITE 179 179 /note="For ATPase activity" E
BINDING 401 401 /ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_note="catalytic; for nuclease activity"		 Magnesium D
SITE 46 46 /note="ATP-binding" Y

Additional information [?]

Size range 540-720 amino acids
Related rules None
Fusion Nter: None Cter: None



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