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Protein

Terminase, large subunit gp2

Gene

2

Organism
Bacillus phage SPP1 (Bacteriophage SPP1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 to initiate and to end a packaging reaction (PubMed:10930407). 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 (packaging sequence), and a large terminase subunit possessing endonucleolytic and ATPase activities. Both terminase subunits heterooligomerize and are docked on the portal protein to form the packaging machine. The terminase large subunit exhibits endonuclease activity and cleaves the viral genome concatemer once the capsid is full (headful packaging). Once the capsid is packaged with the DNA, the terminase complex is substituted by the adapter (gp15) and the stopper protein (gp16) that form the connector.1 Publication2 Publications

Cofactori

Mn2+1 Publication, Mg2+1 PublicationNote: Binds 2 divalent metal cations per subunit. Optimum concentration of Mg2+ is 10 mm (PubMed:10930407). As the Mn2+ dose increases, gp2 converts supercoiled circular plasmid DNA to nicked open circular DNA, subsequently to linear DNA and finally to completely degraded DNA (PubMed:19444313).2 Publications

pH dependencei

Optimum pH is 7.8.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei135 – 1351For ATPase activitySequence analysis
Metal bindingi266 – 2661Manganese or magnesium 1; catalytic; for nuclease activityCombined sources1 Publication
Metal bindingi266 – 2661Manganese or magnesium 2; catalytic; for nuclease activity1 Publication
Metal bindingi321 – 3211Manganese or magnesium 1; catalytic; for nuclease activityCombined sources1 Publication
Metal bindingi400 – 4001Manganese or magnesium 2; catalytic; for nuclease activity1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Viral genome packaging, Virus exit from host cell

Keywords - Ligandi

Magnesium, Manganese, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Terminase, large subunit gp2 (EC:3.1.-.-2 Publications)
Alternative name(s):
DNA-packaging protein G2P
Gene product 2
Short name:
gp2
Gene namesi
Name:2
OrganismiBacillus phage SPP1 (Bacteriophage SPP1)
Taxonomic identifieri10724 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesSiphoviridaeLambdalikevirusunclassified Lambda-like viruses
Virus hostiBacillus subtilis [TaxID: 1423]
Proteomesi
  • UP000002559 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi266 – 2661D → N: Complete loss of endonuclease activity.
Mutagenesisi321 – 3211D → N: Complete loss of endonuclease activity.
Mutagenesisi400 – 4001H → A: Decreased endonuclease activity.
Mutagenesisi403 – 4031D → N: Complete loss of endonuclease activity.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 422422Terminase, large subunit gp2PRO_0000077789Add
BLAST

Interactioni

Subunit structurei

Monomer. Interacts with the terminase small subunit gp1; the active complex is probably heterooligomeric.1 Publication

Structurei

Secondary structure

1
422
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi243 – 2453Combined sources
Helixi252 – 2576Combined sources
Beta strandi261 – 2666Combined sources
Beta strandi274 – 2829Combined sources
Turni283 – 2864Combined sources
Beta strandi287 – 29812Combined sources
Helixi301 – 31010Combined sources
Beta strandi318 – 3203Combined sources
Helixi325 – 3339Combined sources
Beta strandi340 – 3423Combined sources
Helixi347 – 3493Combined sources
Helixi350 – 3589Combined sources
Beta strandi360 – 3656Combined sources
Turni367 – 3693Combined sources
Helixi371 – 3799Combined sources
Beta strandi382 – 3843Combined sources
Beta strandi386 – 3883Combined sources
Beta strandi390 – 3945Combined sources
Beta strandi396 – 3983Combined sources
Helixi400 – 4089Combined sources
Helixi410 – 4123Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2WBNX-ray1.90A232-422[»]
2WC9X-ray2.50A232-422[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP54308.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 198198ATPase activityAdd
BLAST
Regioni232 – 422191Nuclease activityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi33 – 408Walker A motif
Motifi130 – 1356Walker B motif

Family and domain databases

InterProiIPR006437. Phage_terminase_lsu.
[Graphical view]
PfamiPF04466. Terminase_3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01547. phage_term_2. 1 hit.

Sequencei

Sequence statusi: Complete.

P54308-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKVRLSEKF TPHFLEVWRT VKAAQHLKYV LKGGRGSAKS THIAMWIILL
60 70 80 90 100
MMMMPITFLV IRRVYNTVEQ SVFEQLKEAI DMLEVGHLWK VSKSPLRLTY
110 120 130 140 150
IPRGNSIIFR GGDDVQKIKS IKASKFPVAG MWIEELAEFK TEEEVSVIEK
160 170 180 190 200
SVLRAELPPG CRYIFFYSYN PPKRKQSWVN KVFNSSFLPA NTFVDHSTYL
210 220 230 240 250
QNPFLSKAFI EEAEEVKRRN ELKYRHEYLG EALGSGVVPF ENLQIEEGII
260 270 280 290 300
TDAEVARFDN IRQGLDFGYG PDPLAFVRWH YDKRKNRIYA IDELVDHKVS
310 320 330 340 350
LKRTADFVRK NKYESARIIA DSSEPRSIDA LKLEHGINRI EGAKKGPDSV
360 370 380 390 400
EHGERWLDEL DAIVIDPLRT PNIAREFENI DYQTDKNGDP IPRLEDKDNH
410 420
TIDATRYAFE RDMKKGGVSL WG
Length:422
Mass (Da):48,841
Last modified:October 1, 1996 - v1
Checksum:i55D16BDB32239A5C
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti18 – 181W → R in isolate Ts6M; temperature-sensitive.
Natural varianti73 – 731F → L in isolate SUS19.
Natural varianti233 – 2331L → F in isolate SUS19.
Natural varianti412 – 4121D → N in isolate Ts10M; temperature-sensitive.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56064 Genomic DNA. Translation: CAA39537.1.
X97918 Genomic DNA. Translation: CAA66573.1.
PIRiS24451.
RefSeqiNP_690654.1. NC_004166.2.

Genome annotation databases

GeneIDi955254.
KEGGivg:955254.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56064 Genomic DNA. Translation: CAA39537.1.
X97918 Genomic DNA. Translation: CAA66573.1.
PIRiS24451.
RefSeqiNP_690654.1. NC_004166.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2WBNX-ray1.90A232-422[»]
2WC9X-ray2.50A232-422[»]
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi955254.
KEGGivg:955254.

Miscellaneous databases

EvolutionaryTraceiP54308.

Family and domain databases

InterProiIPR006437. Phage_terminase_lsu.
[Graphical view]
PfamiPF04466. Terminase_3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01547. phage_term_2. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular analysis of the Bacillus subtilis bacteriophage SPP1 region encompassing genes 1 to 6. The products of gene 1 and gene 2 are required for pac cleavage."
    Chai S., Bravo A., Lueder G., Nedlin A., Trautner T.A., Alonso J.C.
    J. Mol. Biol. 224:87-102(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1."
    Alonso J.C., Luder G., Stiege A.C., Chai S., Weise F., Trautner T.A.
    Gene 204:201-212(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "Functional analysis of the terminase large subunit, G2P, of Bacillus subtilis bacteriophage SPP1."
    Gual A., Camacho A.G., Alonso J.C.
    J. Biol. Chem. 275:35311-35319(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR.
  4. "Bacillus subtilis bacteriophage SPP1 DNA packaging motor requires terminase and portal proteins."
    Camacho A.G., Gual A., Lurz R., Tavares P., Alonso J.C.
    J. Biol. Chem. 278:23251-23259(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  5. "The bacteriophage DNA packaging motor."
    Rao V.B., Feiss M.
    Annu. Rev. Genet. 42:647-681(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  6. "Headful DNA packaging: bacteriophage SPP1 as a model system."
    Oliveira L., Tavares P., Alonso J.C.
    Virus Res. 173:247-259(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "The nuclease domain of the SPP1 packaging motor coordinates DNA cleavage and encapsidation."
    Cornilleau C., Atmane N., Jacquet E., Smits C., Alonso J.C., Tavares P., Oliveira L.
    Nucleic Acids Res. 41:340-354(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR.
  8. "Structural basis for the nuclease activity of a bacteriophage large terminase."
    Smits C., Chechik M., Kovalevskiy O.V., Shevtsov M.B., Foster A.W., Alonso J.C., Antson A.A.
    EMBO Rep. 10:592-598(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 232-422 IN COMPLEX WITH MANGANESE, MUTAGENESIS OF ASP-266; ASP-321 AND ASP-403, COFACTOR.

Entry informationi

Entry nameiTERL_BPSPP
AccessioniPrimary (citable) accession number: P54308
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: February 17, 2016
This is version 74 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.