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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "HYDROLASE,TRANSFERASE/DNA"

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Search Summary

This query matches 15 Structures.

Refinements

Structure Determination Methodology

experimental (15)

Scientific Name of Source Organism

	Escherichia phage T7 (9)
	Mus musculus (5)
	synthetic construct (2)
	Escherichia phage RB69 (1)

Taxonomy

	Duplodnaviria (10)
	Eukaryota (5)
	other sequences (2)

Experimental Method

	ELECTRON MICROSCOPY (9)
	X-RAY DIFFRACTION (6)

Polymer Entity Type

	DNA (15)
	Protein (15)
	RNA (4)

Refinement Resolution (Å)

	1.5 - 2.0 (2)
	2.0 - 2.5 (3)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)
	3.5 - 4.0 (4)
	4.0 - 4.5 (3)
	> 4.5 (1)

Release Date

	2010 - 2014 (6)
	2015 - 2019 (9)

Enzyme Classification Name

	Hydrolases (15)
	Transferases (15)

Symmetry Type

Asymmetric (15)

SCOP Classification

	Alpha and beta proteins (a/b) (1)
	Multi-domain proteins (alpha and beta) (1)

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1 to 15 of 15 Structures

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3U7F \| pdb_00003u7f	Download File View File

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTCp)

Coquelle, N., Havali, Z., Bernstein, N., Green, R., Glover, J.N.M.

(2011) Proc Natl Acad Sci U S A 108: 21022-21027

Released	2011-12-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Mus musculus
Macromolecule	Bifunctional polynucleotide phosphatase/kinase (protein) DNA (nucleic acid)
Unique Ligands	GOL, MG, PO4

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3U7G \| pdb_00003u7g	Download File View File

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTAp)

Coquelle, N., Havali, Z., Bernstein, N., Green, R., Glover, J.N.M.

(2011) Proc Natl Acad Sci U S A 108: 21022-21027

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	Bifunctional polynucleotide phosphatase/kinase (protein) DNA (nucleic acid)
Unique Ligands	GOL, MG, PO4

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3U7H \| pdb_00003u7h	Download File View File

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTTp)

Coquelle, N., Havali, Z., Bernstein, N., Green, R., Glover, J.N.M.

(2011) Proc Natl Acad Sci U S A 108: 21022-21027

Released	2011-12-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	Bifunctional polynucleotide phosphatase/kinase (protein) DNA (nucleic acid)
Unique Ligands	GOL, MG, PO4

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3ZVM \| pdb_00003zvm	Download File View File

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

Garces, F., Pearl, L.H., Oliver, A.W.

(2011) Mol Cell 44: 385-396

Released	2011-11-16
Method	X-RAY DIFFRACTION 1.997 Å
Organisms	Mus musculus synthetic construct
Macromolecule	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE (protein) 5'-D(GPTPCPAP*CP)-3' (nucleic acid)
Unique Ligands	ACT, ADP, EPE, GOL, MG

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3ZVN \| pdb_00003zvn	Download File View File

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

Garces, F., Pearl, L.H., Oliver, A.W.

(2011) Mol Cell 44: 385-396

Released	2011-11-16
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Mus musculus synthetic construct
Macromolecule	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE (protein) 5'-D(GPTPCPAP*CP)-3' (nucleic acid)
Unique Ligands	ADP, GOL, MN

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4KHN \| pdb_00004khn	Download File View File

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

Guja, K.E., Jacewicz, A., Trzemecka, A., Plochocka, D., Yakubovskaya, E., Bebenek, A., Garcia-Diaz, M.

(2013) PLoS One 8: e76700-e76700

Released	2013-10-09
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Escherichia phage RB69
Macromolecule	DNA polymerase (protein) DNA (5'-D(GPCPGPGPAPCPTPGPCPTPTPAPC)-3') (nucleic acid) DNA (5'-D(TPCPAPCPGPTPAPAPGPCPAPGPTPCPCPGPCP*G)-3') (nucleic acid)
Unique Ligands	CA, GOL, NA, SO4, XG4

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6N7I \| pdb_00006n7i	Download File View File

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (gp4(5)-DNA)

Gao, Y., Cui, Y., Zhou, Z., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 3.2 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA (25-MER) (nucleic acid)
Unique Ligands	MG, TTP

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6N7N \| pdb_00006n7n	Download File View File

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form I)

Gao, Y., Cui, Y., Zhou, Z., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTP*T)-3') (nucleic acid)
Unique Ligands	MG, TTP

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6N7S \| pdb_00006n7s	Download File View File

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form II)

Gao, Y., Cui, Y., Zhou, Z., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 4.6 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA (25-MER) (nucleic acid)
Unique Ligands	MG, TTP

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6N7T \| pdb_00006n7t	Download File View File

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form III)

Gao, Y., Cui, Y., Zhou, Z., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 3.9 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA (25-MER) (nucleic acid)
Unique Ligands	MG, TTP

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6N7V \| pdb_00006n7v	Download File View File

Structure of bacteriophage T7 gp4 (helicase-primase, E343Q mutant) in complex with ssDNA, dTTP, AC dinucleotide, and CTP (from multiple lead complexes)

Gao, Y., Fox, T., Val, N., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA (93-MER) (nucleic acid)
Unique Ligands	MG, TTP

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6N9U \| pdb_00006n9u	Download File View File

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with primase domains of two gp4 subunits bound to an RNA/DNA hybrid and dTTP (from LagS1)

Gao, Y., Fox, T., Val, N., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 3.7 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA-directed DNA polymerase (protein) DNA (44-MER) (nucleic acid) RNA (5'-R(APCPCPAPG)-D(P(DOC))-3') (nucleic acid)
Unique Ligands	MG, TTP, ZN

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6N9V \| pdb_00006n9v	Download File View File

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS1)

Gao, Y., Fox, T., Val, N., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA-directed DNA polymerase (protein) Primer (nucleic acid) Template (nucleic acid)
Unique Ligands	MG, TTP, ZN

Explore in 3D

6N9W \| pdb_00006n9w	Download File View File

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS2)

Gao, Y., Cui, Y., Zhou, Z., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 4 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA-directed DNA polymerase (protein) Primer (nucleic acid) Template (nucleic acid)
Unique Ligands	MG, TTP, ZN

Explore in 3D

6N9X \| pdb_00006n9x	Download File View File

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)

Gao, Y., Fox, T., Val, N., Yang, W.

(2019) Science 363:

Released	2019-03-06
Method	ELECTRON MICROSCOPY 4.1 Å
Organisms	Escherichia phage T7
Macromolecule	DNA primase/helicase (protein) DNA-directed DNA polymerase (protein) Primer (nucleic acid) Template (nucleic acid)
Unique Ligands	MG, TTP, ZN

1 to 15 of 15 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

3U7F | pdb_00003u7f

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTCp)

3U7G | pdb_00003u7g

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTAp)

3U7H | pdb_00003u7h

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTTp)

3ZVM | pdb_00003zvm

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

3ZVN | pdb_00003zvn

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

4KHN | pdb_00004khn

Crystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase

6N7I | pdb_00006n7i

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (gp4(5)-DNA)

6N7N | pdb_00006n7n

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form I)

6N7S | pdb_00006n7s

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form II)

6N7T | pdb_00006n7t

Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form III)

6N7V | pdb_00006n7v

Structure of bacteriophage T7 gp4 (helicase-primase, E343Q mutant) in complex with ssDNA, dTTP, AC dinucleotide, and CTP (from multiple lead complexes)

6N9U | pdb_00006n9u

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with primase domains of two gp4 subunits bound to an RNA/DNA hybrid and dTTP (from LagS1)

6N9V | pdb_00006n9v

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS1)

6N9W | pdb_00006n9w

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS2)

6N9X | pdb_00006n9x

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

3U7F | pdb_00003u7f

3U7G | pdb_00003u7g

3U7H | pdb_00003u7h

3ZVM | pdb_00003zvm

3ZVN | pdb_00003zvn

4KHN | pdb_00004khn

6N7I | pdb_00006n7i

6N7N | pdb_00006n7n

6N7S | pdb_00006n7s

6N7T | pdb_00006n7t

6N7V | pdb_00006n7v

6N9U | pdb_00006n9u

6N9V | pdb_00006n9v

6N9W | pdb_00006n9w

6N9X | pdb_00006n9x