Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2EX3

Bacteriophage phi29 DNA polymerase bound to terminal protein

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0001882	molecular_function	nucleoside binding
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0004518	molecular_function	nuclease activity
A	0004527	molecular_function	exonuclease activity
A	0006260	biological_process	DNA replication
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0034061	molecular_function	DNA polymerase activity
A	0039693	biological_process	viral DNA genome replication
A	0046872	molecular_function	metal ion binding
B	0006260	biological_process	DNA replication
B	0006269	biological_process	DNA replication, synthesis of primer
C	0000166	molecular_function	nucleotide binding
C	0001882	molecular_function	nucleoside binding
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0004518	molecular_function	nuclease activity
C	0004527	molecular_function	exonuclease activity
C	0006260	biological_process	DNA replication
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0034061	molecular_function	DNA polymerase activity
C	0039693	biological_process	viral DNA genome replication
C	0046872	molecular_function	metal ion binding
D	0006260	biological_process	DNA replication
D	0006269	biological_process	DNA replication, synthesis of primer
E	0000166	molecular_function	nucleotide binding
E	0001882	molecular_function	nucleoside binding
E	0003676	molecular_function	nucleic acid binding
E	0003677	molecular_function	DNA binding
E	0003887	molecular_function	DNA-directed DNA polymerase activity
E	0004518	molecular_function	nuclease activity
E	0004527	molecular_function	exonuclease activity
E	0006260	biological_process	DNA replication
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0016787	molecular_function	hydrolase activity
E	0034061	molecular_function	DNA polymerase activity
E	0039693	biological_process	viral DNA genome replication
E	0046872	molecular_function	metal ion binding
F	0006260	biological_process	DNA replication
F	0006269	biological_process	DNA replication, synthesis of primer
G	0000166	molecular_function	nucleotide binding
G	0001882	molecular_function	nucleoside binding
G	0003676	molecular_function	nucleic acid binding
G	0003677	molecular_function	DNA binding
G	0003887	molecular_function	DNA-directed DNA polymerase activity
G	0004518	molecular_function	nuclease activity
G	0004527	molecular_function	exonuclease activity
G	0006260	biological_process	DNA replication
G	0016740	molecular_function	transferase activity
G	0016779	molecular_function	nucleotidyltransferase activity
G	0016787	molecular_function	hydrolase activity
G	0034061	molecular_function	DNA polymerase activity
G	0039693	biological_process	viral DNA genome replication
G	0046872	molecular_function	metal ion binding
H	0006260	biological_process	DNA replication
H	0006269	biological_process	DNA replication, synthesis of primer
I	0000166	molecular_function	nucleotide binding
I	0001882	molecular_function	nucleoside binding
I	0003676	molecular_function	nucleic acid binding
I	0003677	molecular_function	DNA binding
I	0003887	molecular_function	DNA-directed DNA polymerase activity
I	0004518	molecular_function	nuclease activity
I	0004527	molecular_function	exonuclease activity
I	0006260	biological_process	DNA replication
I	0016740	molecular_function	transferase activity
I	0016779	molecular_function	nucleotidyltransferase activity
I	0016787	molecular_function	hydrolase activity
I	0034061	molecular_function	DNA polymerase activity
I	0039693	biological_process	viral DNA genome replication
I	0046872	molecular_function	metal ion binding
J	0006260	biological_process	DNA replication
J	0006269	biological_process	DNA replication, synthesis of primer
K	0000166	molecular_function	nucleotide binding
K	0001882	molecular_function	nucleoside binding
K	0003676	molecular_function	nucleic acid binding
K	0003677	molecular_function	DNA binding
K	0003887	molecular_function	DNA-directed DNA polymerase activity
K	0004518	molecular_function	nuclease activity
K	0004527	molecular_function	exonuclease activity
K	0006260	biological_process	DNA replication
K	0016740	molecular_function	transferase activity
K	0016779	molecular_function	nucleotidyltransferase activity
K	0016787	molecular_function	hydrolase activity
K	0034061	molecular_function	DNA polymerase activity
K	0039693	biological_process	viral DNA genome replication
K	0046872	molecular_function	metal ion binding
L	0006260	biological_process	DNA replication
L	0006269	biological_process	DNA replication, synthesis of primer

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB A 701

Chain	Residue
A	ASP169

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PB A 702

Chain	Residue
A	GLU14
A	ASP145
A	TYR148
A	ASP169

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB A 703

Chain	Residue
A	GLU221

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB C 704

Chain	Residue
C	ASP169

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB C 705

Chain	Residue
C	GLU14
C	ASP169

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB E 707

Chain	Residue
E	GLU14
E	ASP169

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB E 708

Chain	Residue
E	ASP169

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB G 710

Chain	Residue
G	ASP169

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PB G 711

Chain	Residue
G	GLU14
G	ASP145
G	TYR148
G	ASP169

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB G 712

Chain	Residue
G	GLU221

site_id	BC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB I 713

Chain	Residue
I	ASP169

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB I 714

Chain	Residue
I	GLU14
I	ASP169

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB K 715

Chain	Residue
K	GLU14
K	ASP169

site_id	BC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB K 716

Chain	Residue
K	ASP169

Functional Information from PROSITE/UniProt

site_id	PS00116
Number of Residues	9
Details	DNA_POLYMERASE_B DNA polymerase family B signature. YCDTDSIHL

Chain	Residue	Details
A	TYR454-LEU462

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	SITE: Positions the 3' end of the template strand at the active site of the DNA polymerase => ECO:0000269\|PubMed:26400085

Chain	Residue	Details
B	PHE230
I	ASP169
K	ASP145
K	ASP169
D	PHE230
F	PHE230
H	PHE230
J	PHE230
L	PHE230
G	ASP145
G	ASP169
I	ASP145

site_id	SWS_FT_FI2
Number of Residues	6
Details	MOD_RES: O-(5'-phospho-DNA)-serine => ECO:0000269\|PubMed:6779279

Chain	Residue	Details
B	SER232
D	SER232
F	SER232
H	SER232
J	SER232
L	SER232

site_id	SWS_FT_FI3
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:19883660, ECO:0007744\|PDB:2PYJ

Chain	Residue	Details
A	VAL250
C	VAL250
E	VAL250
G	VAL250
I	VAL250
K	VAL250

site_id	SWS_FT_FI4
Number of Residues	24
Details	BINDING: BINDING => ECO:0007744\|PDB:2PYL

Chain	Residue	Details
A	TYR254
E	LYS371
E	LYS383
E	ASP458
G	TYR254
G	LYS371
G	LYS383
G	ASP458
I	TYR254
I	LYS371
I	LYS383
A	LYS371
I	ASP458
K	TYR254
K	LYS371
K	LYS383
K	ASP458
A	LYS383
A	ASP458
C	TYR254
C	LYS371
C	LYS383
C	ASP458
E	TYR254

site_id	SWS_FT_FI5
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:9784372

Chain	Residue	Details
A	ASP456
C	ASP456
E	ASP456
G	ASP456
I	ASP456
K	ASP456

site_id	SWS_FT_FI6
Number of Residues	18
Details	SITE: Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:2790959, ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ALA12
G	ALA12
G	GLU14
G	ALA66
I	ALA12
I	GLU14
I	ALA66
K	ALA12
K	GLU14
K	ALA66
A	GLU14
A	ALA66
C	ALA12
C	GLU14
C	ALA66
E	ALA12
E	GLU14
E	ALA66

site_id	SWS_FT_FI7
Number of Residues	12
Details	SITE: Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site => ECO:0000269\|PubMed:8605889

Chain	Residue	Details
A	THR15
I	ASN62
K	THR15
K	ASN62
A	ASN62
C	THR15
C	ASN62
E	THR15
E	ASN62
G	THR15
G	ASN62
I	THR15

site_id	SWS_FT_FI8
Number of Residues	18
Details	SITE: Interaction with the primer terminal protein => ECO:0000269\|PubMed:11884636

Chain	Residue	Details
A	TYR59
G	TYR59
G	HIS61
G	PHE69
I	TYR59
I	HIS61
I	PHE69
K	TYR59
K	HIS61
K	PHE69
A	HIS61
A	PHE69
C	TYR59
C	HIS61
C	PHE69
E	TYR59
E	HIS61
E	PHE69

site_id	SWS_FT_FI9
Number of Residues	18
Details	SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:9786901

Chain	Residue	Details
A	PHE65
G	PHE65
G	SER122
G	LEU123
I	PHE65
I	SER122
I	LEU123
K	PHE65
K	SER122
K	LEU123
A	SER122
A	LEU123
C	PHE65
C	SER122
C	LEU123
E	PHE65
E	SER122
E	LEU123

site_id	SWS_FT_FI10
Number of Residues	6
Details	SITE: Involved in binding template-primer structures => ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ILE93
C	ILE93
E	ILE93
G	ILE93
I	ILE93
K	ILE93

site_id	SWS_FT_FI11
Number of Residues	6
Details	SITE: Involved in the stabilization of the frayed 3' terminus at the exonuclease active site => ECO:0000269\|PubMed:19576228

Chain	Residue	Details
A	TYR148
C	TYR148
E	TYR148
G	TYR148
I	TYR148
K	TYR148

site_id	SWS_FT_FI12
Number of Residues	6
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:8226957

Chain	Residue	Details
A	SER252
C	SER252
E	SER252
G	SER252
I	SER252
K	SER252

site_id	SWS_FT_FI13
Number of Residues	12
Details	SITE: Probably involved in nucleotide binding selection => ECO:0000269\|PubMed:8537389

Chain	Residue	Details
A	TYR254
I	TYR390
K	TYR254
K	TYR390
A	TYR390
C	TYR254
C	TYR390
E	TYR254
E	TYR390
G	TYR254
G	TYR390
I	TYR254

site_id	SWS_FT_FI14
Number of Residues	12
Details	SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:8605889

Chain	Residue	Details
A	THR356
I	GLU420
K	THR356
K	GLU420
A	GLU420
C	THR356
C	GLU420
E	THR356
E	GLU420
G	THR356
G	GLU420
I	THR356

site_id	SWS_FT_FI15
Number of Residues	6
Details	SITE: Involved in the binding of DNA and dNTP => ECO:0000269\|PubMed:11917008

Chain	Residue	Details
A	ILE364
C	ILE364
E	ILE364
G	ILE364
I	ILE364
K	ILE364

site_id	SWS_FT_FI16
Number of Residues	12
Details	SITE: Stabilization of the incoming nucleotide => ECO:0000269\|PubMed:14672657

Chain	Residue	Details
A	LYS366
I	LYS379
K	LYS366
K	LYS379
A	LYS379
C	LYS366
C	LYS379
E	LYS366
E	LYS379
G	LYS366
G	LYS379
I	LYS366

site_id	SWS_FT_FI17
Number of Residues	6
Details	SITE: Interacts with the phosphate groups of the incoming nucleotide => ECO:0000269\|PubMed:11917008

Chain	Residue	Details
A	LYS371
C	LYS371
E	LYS371
G	LYS371
I	LYS371
K	LYS371

site_id	SWS_FT_FI18
Number of Residues	6
Details	SITE: Probably involved in nucleotide binding selection => ECO:0000269\|PubMed:9199402

Chain	Residue	Details
A	LYS383
C	LYS383
E	LYS383
G	LYS383
I	LYS383
K	LYS383

site_id	SWS_FT_FI19
Number of Residues	6
Details	SITE: Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity => ECO:0000269\|PubMed:12805385

Chain	Residue	Details
A	LEU384
C	LEU384
E	LEU384
G	LEU384
I	LEU384
K	LEU384

site_id	SWS_FT_FI20
Number of Residues	12
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ASN387
I	GLY391
K	ASN387
K	GLY391
A	GLY391
C	ASN387
C	GLY391
E	ASN387
E	GLY391
G	ASN387
G	GLY391
I	ASN387

site_id	SWS_FT_FI21
Number of Residues	12
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:7962004

Chain	Residue	Details
A	THR434
I	ARG438
K	THR434
K	ARG438
A	ARG438
C	THR434
C	ARG438
E	THR434
E	ARG438
G	THR434
G	ARG438
I	THR434

site_id	SWS_FT_FI22
Number of Residues	12
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:7852344

Chain	Residue	Details
A	LYS498
I	TYR500
K	LYS498
K	TYR500
A	TYR500
C	LYS498
C	TYR500
E	LYS498
E	TYR500
G	LYS498
G	TYR500
I	LYS498

site_id	SWS_FT_FI23
Number of Residues	6
Details	SITE: Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities => ECO:0000269\|PubMed:24023769

Chain	Residue	Details
A	LYS529
C	LYS529
E	LYS529
G	LYS529
I	LYS529
K	LYS529

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)