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Protein

DNA polymerase

Gene

2

Organism
Bacillus phage phi29 (Bacteriophage phi-29)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Replicates the viral genomic DNA. This polymerase possesses three enzymatic activities: DNA synthesis (polymerase), terminal protein (TP) deoxynucleotidylation, which is the formation of a covalent linkage (phosphoester) between the hydroxyl group of a specific serine residue in TP and 5'-dNMP and 3' to 5' exonuclease activity. Exonuclease activity has a proofreading purpose.2 Publications

Catalytic activityi

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).

Cofactori

Mg2+1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei122 – 1221Critical for 3'-5' exonucleolysis
Metal bindingi145 – 1451MagnesiumCombined sources1 Publication
Metal bindingi169 – 1691MagnesiumCombined sources1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication, Viral DNA replication

Keywords - Ligandi

DNA-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA polymerase (EC:2.7.7.7, EC:3.1.11.-1 Publication)
Alternative name(s):
Early protein GP2
Gene namesi
Name:2
OrganismiBacillus phage phi29 (Bacteriophage phi-29)
Taxonomic identifieri10756 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesPodoviridaePicovirinaePhi29likevirus
Virus hostiBacillus subtilis [TaxID: 1423]
Proteomesi
  • UP000001207 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi12 – 121D → A: Loss of exonuclease activity. 1 Publication
Mutagenesisi14 – 141E → A: Loss of exonuclease activity. 1 Publication
Mutagenesisi65 – 651F → S: Loss of capacity to interact with a DNA primer/template structure. 1 Publication
Mutagenesisi66 – 661D → A: Loss of exonuclease activity. 1 Publication
Mutagenesisi122 – 1221S → T: Loss of capacity to interact with a DNA primer/template structure. 1 Publication
Mutagenesisi123 – 1231L → N: Loss of capacity to interact with a DNA primer/template structure. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 575575DNA polymerasePRO_0000046542Add
BLAST

Expressioni

Keywords - Developmental stagei

Early protein

Structurei

Secondary structure

1
575
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 158Combined sources
Beta strandi19 – 213Combined sources
Beta strandi24 – 3310Combined sources
Beta strandi38 – 425Combined sources
Helixi44 – 5411Combined sources
Beta strandi57 – 626Combined sources
Helixi63 – 7614Combined sources
Beta strandi89 – 957Combined sources
Beta strandi100 – 11011Combined sources
Beta strandi113 – 1219Combined sources
Helixi122 – 1254Combined sources
Helixi130 – 1367Combined sources
Beta strandi148 – 1503Combined sources
Helixi160 – 18223Combined sources
Beta strandi187 – 1893Combined sources
Helixi190 – 20213Combined sources
Helixi204 – 2107Combined sources
Helixi216 – 2238Combined sources
Beta strandi231 – 2333Combined sources
Helixi235 – 2373Combined sources
Beta strandi238 – 2425Combined sources
Beta strandi244 – 2507Combined sources
Helixi253 – 2608Combined sources
Beta strandi263 – 27412Combined sources
Beta strandi283 – 29412Combined sources
Beta strandi308 – 3103Combined sources
Beta strandi324 – 3296Combined sources
Helixi330 – 33910Combined sources
Beta strandi340 – 35718Combined sources
Helixi361 – 37313Combined sources
Helixi376 – 38712Combined sources
Helixi390 – 3934Combined sources
Beta strandi401 – 4066Combined sources
Beta strandi410 – 4167Combined sources
Helixi427 – 44721Combined sources
Turni448 – 4514Combined sources
Beta strandi452 – 4565Combined sources
Beta strandi459 – 4668Combined sources
Helixi469 – 4746Combined sources
Beta strandi477 – 4793Combined sources
Beta strandi482 – 49615Combined sources
Beta strandi499 – 50911Combined sources
Beta strandi512 – 5154Combined sources
Beta strandi518 – 5203Combined sources
Beta strandi522 – 5309Combined sources
Helixi535 – 5384Combined sources
Turni543 – 5453Combined sources
Beta strandi551 – 56111Combined sources
Beta strandi564 – 57310Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XHXX-ray2.35A/B/C/D1-575[»]
1XHZX-ray2.70A/B/C/D1-575[»]
1XI1X-ray2.20A/B1-575[»]
2EX3X-ray3.00A/C/E/G/I/K1-575[»]
2PY5X-ray1.60A/B1-575[»]
2PYJX-ray2.03A/B1-575[»]
2PYLX-ray2.20A1-575[»]
2PZSX-ray2.60A/B/C/D1-575[»]
ProteinModelPortaliP03680.
SMRiP03680. Positions 5-575.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03680.

Family & Domainsi

Sequence similaritiesi

Belongs to the DNA polymerase type-B family.Curated

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
InterProiIPR006172. DNA-dir_DNA_pol_B.
IPR017964. DNA-dir_DNA_pol_B_CS.
IPR004868. DNA-dir_DNA_pol_B_mt/vir.
IPR014416. DNA-dir_DNA_polB_phi29_vir.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF03175. DNA_pol_B_2. 1 hit.
[Graphical view]
PIRSFiPIRSF004178. Dpol_Bac_phage. 1 hit.
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P03680-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKHMPRKMYS CDFETTTKVE DCRVWAYGYM NIEDHSEYKI GNSLDEFMAW
60 70 80 90 100
VLKVQADLYF HNLKFDGAFI INWLERNGFK WSADGLPNTY NTIISRMGQW
110 120 130 140 150
YMIDICLGYK GKRKIHTVIY DSLKKLPFPV KKIAKDFKLT VLKGDIDYHK
160 170 180 190 200
ERPVGYKITP EEYAYIKNDI QIIAEALLIQ FKQGLDRMTA GSDSLKGFKD
210 220 230 240 250
IITTKKFKKV FPTLSLGLDK EVRYAYRGGF TWLNDRFKEK EIGEGMVFDV
260 270 280 290 300
NSLYPAQMYS RLLPYGEPIV FEGKYVWDED YPLHIQHIRC EFELKEGYIP
310 320 330 340 350
TIQIKRSRFY KGNEYLKSSG GEIADLWLSN VDLELMKEHY DLYNVEYISG
360 370 380 390 400
LKFKATTGLF KDFIDKWTYI KTTSEGAIKQ LAKLMLNSLY GKFASNPDVT
410 420 430 440 450
GKVPYLKENG ALGFRLGEEE TKDPVYTPMG VFITAWARYT TITAAQACYD
460 470 480 490 500
RIIYCDTDSI HLTGTEIPDV IKDIVDPKKL GYWAHESTFK RAKYLRQKTY
510 520 530 540 550
IQDIYMKEVD GKLVEGSPDD YTDIKFSVKC AGMTDKIKKE VTFENFKVGF
560 570
SRKMKPKPVQ VPGGVVLVDD TFTIK
Length:575
Mass (Da):66,714
Last modified:July 21, 1986 - v1
Checksum:i856EEB6B04A7E268
GO

Sequence cautioni

The sequence ACE96023.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti176 – 1761A → R in mutant TS2(24).
Natural varianti355 – 3551A → V in mutant TS2(24).

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01155 Genomic DNA. Translation: CAA24480.1.
EU771092 Genomic DNA. Translation: ACE96023.1. Different initiation.
X53371 Genomic DNA. Translation: CAA37451.1.
PIRiA04282. ERBP29.
RefSeqiYP_002004529.1. NC_011048.1.

Genome annotation databases

GeneIDi6446511.
KEGGivg:6446511.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01155 Genomic DNA. Translation: CAA24480.1.
EU771092 Genomic DNA. Translation: ACE96023.1. Different initiation.
X53371 Genomic DNA. Translation: CAA37451.1.
PIRiA04282. ERBP29.
RefSeqiYP_002004529.1. NC_011048.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XHXX-ray2.35A/B/C/D1-575[»]
1XHZX-ray2.70A/B/C/D1-575[»]
1XI1X-ray2.20A/B1-575[»]
2EX3X-ray3.00A/C/E/G/I/K1-575[»]
2PY5X-ray1.60A/B1-575[»]
2PYJX-ray2.03A/B1-575[»]
2PYLX-ray2.20A1-575[»]
2PZSX-ray2.60A/B/C/D1-575[»]
ProteinModelPortaliP03680.
SMRiP03680. Positions 5-575.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi6446511.
KEGGivg:6446511.

Miscellaneous databases

EvolutionaryTraceiP03680.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
3.90.1600.10. 2 hits.
InterProiIPR006172. DNA-dir_DNA_pol_B.
IPR017964. DNA-dir_DNA_pol_B_CS.
IPR004868. DNA-dir_DNA_pol_B_mt/vir.
IPR014416. DNA-dir_DNA_polB_phi29_vir.
IPR023211. DNA_pol_palm_dom.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF03175. DNA_pol_B_2. 1 hit.
[Graphical view]
PIRSFiPIRSF004178. Dpol_Bac_phage. 1 hit.
PRINTSiPR00106. DNAPOLB.
SMARTiSM00486. POLBc. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Nucleotide sequence of the major early region of bacteriophage phi 29."
    Yoshikawa H., Ito J.
    Gene 17:323-335(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Villegas A.P., Lingohr E.J., Ceyssens P.-J., Kropinski A.M.
    Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Nucleotide sequence of the early genes 3 and 4 of bacteriophage phi 29."
    Escarmis C., Salas M.
    Nucleic Acids Res. 10:5785-5798(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-85.
  4. "Structural and functional analysis of temperature-sensitive mutants of the phage phi 29 DNA polymerase."
    Blasco M.A., Blanco L., Pares E., Salas M., Bernad A.
    Nucleic Acids Res. 18:4763-4770(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTANT TEMPERATURE-SENSITIVE TS2(24).
  5. "A conserved 3' eukaryotic DNA polymerases."
    Bernad A., Blanco L., Lazaro J.M., Martin G., Salas M.
    Cell 59:219-228(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF ASP-12; GLU-14 AND ASP-66.
  6. "Purification of bacteriophage phi 29 DNA polymerase."
    Lazaro J.M., Blanco L., Salas M.
    Methods Enzymol. 262:42-49(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "Mutational analysis of bacteriophage phi 29 DNA polymerase."
    Blanco L., Salas M.
    Methods Enzymol. 262:283-294(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS.
  8. "phi29 DNA polymerase residue Ser122, a single-stranded DNA ligand for 3'-5' exonucleolysis, is required to interact with the terminal protein."
    de Vega M., Blanco L., Salas M.
    J. Biol. Chem. 273:28966-28977(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF PHE-65; SER-122 AND LEU-123.
  9. "Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29."
    Kamtekar S., Berman A.J., Wang J., Lazaro J.M., de Vega M., Blanco L., Salas M., Steitz T.A.
    Mol. Cell 16:609-618(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS).
  10. "Correction of X-ray intensities from single crystals containing lattice-translocation defects."
    Wang J., Kamtekar S., Berman A.J., Steitz T.A.
    Acta Crystallogr. D 61:67-74(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, COFACTOR.
  11. "The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition."
    Kamtekar S., Berman A.J., Wang J., Lazaro J.M., de Vega M., Blanco L., Salas M., Steitz T.A.
    EMBO J. 25:1335-1343(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS).
  12. "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases."
    Berman A.J., Kamtekar S., Goodman J.L., Lazaro J.M., de Vega M., Blanco L., Salas M., Steitz T.A.
    EMBO J. 26:3494-3505(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH MANGANESE AND TTP, COFACTOR.

Entry informationi

Entry nameiDPOL_BPPH2
AccessioniPrimary (citable) accession number: P03680
Secondary accession number(s): B3VMN6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: October 14, 2015
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

This DNA polymerase requires a protein as a primer.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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.