P03680 (DPOL_BPPH2) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA polymerase
EC=2.7.7.7

Alternative name(s):
Early protein GP2

Gene names

Name:

2

Organism

Bacillus phage phi29 (Bacteriophage phi-29)

Taxonomic identifier

10756 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Caudovirales › Podoviridae › Picovirinae › Phi29-like viruses

Virus host

Bacillus subtilis [TaxID: 1423]

Protein attributes

Sequence length	575 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
Catalytic activity	Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Miscellaneous	This DNA polymerase requires a protein as a primer.
Sequence similarities	Belongs to the DNA polymerase type-B family.

Ontologies

Keywords
Biological process	DNA replication
Developmental stage	Early protein
Ligand	DNA-binding
Molecular function	DNA-directed DNA polymerase Exonuclease Hydrolase Nuclease Nucleotidyltransferase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	3'-5' exonuclease activity Inferred from electronic annotation. Source: InterPro DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW nucleoside binding Inferred from electronic annotation. Source: InterPro nucleotide binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 575

575

DNA polymerase

PRO_0000046542

Sites

Site

122

1

Critical for 3'-5' exonucleolysis

Natural variations

Natural variant

176

1

A → R in mutant TS2(24).

Natural variant

355

1

A → V in mutant TS2(24).

Experimental info

Mutagenesis

65

1

F → S: Loss of capacity to interact with a DNA primer/template structure. Ref.6

Mutagenesis

122

1

S → T: Loss of capacity to interact with a DNA primer/template structure. Ref.6

Mutagenesis

123

1

L → N: Loss of capacity to interact with a DNA primer/template structure. Ref.6

Secondary structure

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575

Helix Strand Turn

Details...

Beta strand

8 – 15

8

Beta strand

19 – 21

3

Beta strand

24 – 31

8

Beta strand

34 – 42

9

Helix

44 – 54

11

Beta strand

56 – 62

7

Helix

63 – 75

13

Turn

76 – 78

3

Beta strand

89 – 94

6

Beta strand

100 – 110

11

Beta strand

113 – 121

9

Helix

122 – 124

3

Helix

130 – 137

8

Beta strand

148 – 150

3

Helix

160 – 181

22

Turn

182 – 184

3

Beta strand

187 – 189

3

Helix

190 – 202

13

Helix

204 – 210

7

Helix

216 – 223

8

Beta strand

231 – 233

3

Helix

235 – 237

3

Beta strand

245 – 250

6

Helix

253 – 260

8

Beta strand

263 – 274

12

Beta strand

283 – 294

12

Beta strand

308 – 310

3

Beta strand

324 – 329

6

Helix

330 – 339

10

Beta strand

340 – 357

18

Helix

361 – 372

12

Helix

376 – 387

12

Helix

389 – 393

5

Beta strand

402 – 406

5

Beta strand

412 – 416

5

Helix

427 – 447

21

Turn

448 – 451

4

Beta strand

452 – 466

15

Helix

469 – 474

6

Beta strand

477 – 479

3

Beta strand

482 – 496

15

Beta strand

499 – 509

11

Beta strand

512 – 515

4

Beta strand

522 – 530

9

Helix

535 – 538

4

Turn

543 – 545

3

Beta strand

551 – 559

9

Beta strand

566 – 573

8

Sequences

	Sequence		Length	Mass (Da)
	P03680 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 856EEB6B04A7E268	FASTA	575	66,714
	10 20 30 40 50 60 MKHMPRKMYS CDFETTTKVE DCRVWAYGYM NIEDHSEYKI GNSLDEFMAW VLKVQADLYF 70 80 90 100 110 120 HNLKFDGAFI INWLERNGFK WSADGLPNTY NTIISRMGQW YMIDICLGYK GKRKIHTVIY 130 140 150 160 170 180 DSLKKLPFPV KKIAKDFKLT VLKGDIDYHK ERPVGYKITP EEYAYIKNDI QIIAEALLIQ 190 200 210 220 230 240 FKQGLDRMTA GSDSLKGFKD IITTKKFKKV FPTLSLGLDK EVRYAYRGGF TWLNDRFKEK 250 260 270 280 290 300 EIGEGMVFDV NSLYPAQMYS RLLPYGEPIV FEGKYVWDED YPLHIQHIRC EFELKEGYIP 310 320 330 340 350 360 TIQIKRSRFY KGNEYLKSSG GEIADLWLSN VDLELMKEHY DLYNVEYISG LKFKATTGLF 370 380 390 400 410 420 KDFIDKWTYI KTTSEGAIKQ LAKLMLNSLY GKFASNPDVT GKVPYLKENG ALGFRLGEEE 430 440 450 460 470 480 TKDPVYTPMG VFITAWARYT TITAAQACYD RIIYCDTDSI HLTGTEIPDV IKDIVDPKKL 490 500 510 520 530 540 GYWAHESTFK RAKYLRQKTY IQDIYMKEVD GKLVEGSPDD YTDIKFSVKC AGMTDKIKKE 550 560 570 VTFENFKVGF SRKMKPKPVQ VPGGVVLVDD TFTIK

References

[1]	"Nucleotide sequence of the major early region of bacteriophage phi 29." Yoshikawa H., Ito J. Gene 17:323-335(1982) [PubMed: 6809534] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"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: 6292852] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-85.
[3]	"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: 2118623] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTANT TEMPERATURE-SENSITIVE TS2(24).
[4]	"Purification of bacteriophage phi 29 DNA polymerase." Lazaro J.M., Blanco L., Salas M. Methods Enzymol. 262:42-49(1995) [PubMed: 8594366] [Abstract] Cited for: CHARACTERIZATION.
[5]	"Mutational analysis of bacteriophage phi 29 DNA polymerase." Blanco L., Salas M. Methods Enzymol. 262:283-294(1995) [PubMed: 8594354] [Abstract] Cited for: MUTAGENESIS.
[6]	"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: 9786901] [Abstract] Cited for: MUTAGENESIS OF PHE-65; SER-122 AND LEU-123.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V01155 Genomic DNA. Translation: CAA24480.1.
X53371 Genomic DNA. Translation: CAA37451.1.

PIR

ERBP29. A04282.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1XHX	X-ray	2.35	A/B/C/D	1-575	[»]
1XHZ	X-ray	2.70	A/B/C/D	1-575	[»]
1XI1	X-ray	2.20	A/B	5-575	[»]
2EX3	X-ray	3.00	A/C/E/G/I/K	1-575	[»]
2PY5	X-ray	1.60	A/B	1-575	[»]
2PYJ	X-ray	2.03	A/B	1-575	[»]
2PYL	X-ray	2.20	A	1-575	[»]
2PZS	X-ray	2.60	A/B/C/D	1-575	[»]

ProteinModelPortal

P03680.

SMR

P03680. Positions 5-575.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR006172. 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]

Gene3D

G3DSA:3.90.1600.10. DNA_pol_palm_dom. 2 hits.

Pfam

PF03175. DNA_pol_B_2. 1 hit.
[Graphical view]

PIRSF

PIRSF004178. Dpol_Bac_phage. 1 hit.

PRINTS

PR00106. DNAPOLB.

SMART

SM00486. POLBc. 1 hit.
[Graphical view]

SUPFAM

SSF53098. RNaseH_fold. 1 hit.

PROSITE

PS00116. DNA_POLYMERASE_B. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DPOL_BPPH2

Accession

Primary (citable) accession number: P03680

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	January 25, 2012
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program