PDBsum entry 1ktq

Nucleotidyltransferase

PDB id

1ktq

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Contents

			Protein chain

					534 a.a. *

			Waters ×1320

* Residue conservation analysis

PDB id:

1ktq

Links

Name:

Nucleotidyltransferase

Title:

DNA polymerase

Structure:

DNA polymerase i. Chain: a. Synonym: klentaq. Engineered: yes

Source:

Thermus aquaticus. Organism_taxid: 271. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.50Å

R-factor:

0.198

R-free:

0.262

Authors:

S.Korolev,G.Waksman

Key ref:

S.Korolev et al. (1995). Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability. Proc Natl Acad Sci U S A, 92, 9264-9268. PubMed id: 7568114 DOI: 10.1073/pnas.92.20.9264

Date:

16-Aug-95

Release date:

08-Nov-96

PROCHECK

	Headers

	References

Protein chain

P19821 (DPO1_THEAQ) - DNA polymerase I, thermostable from Thermus aquaticus

Seq: Struc:

Seq: Struc:					832 a.a. 534 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.2.7.7.7 - DNA-directed Dna polymerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

DNA(n)	+	2'-deoxyribonucleoside 5'-triphosphate	=	DNA(n+1)	+	diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1073/pnas.92.20.9264	Proc Natl Acad Sci U S A 92:9264-9268 (1995)
PubMed id: 7568114

Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability.
S.Korolev, M.Nayal, W.M.Barnes, E.Di Cera, G.Waksman.

ABSTRACT

The crystal structure of the large fragment of the Thermus aquaticus DNA polymerase (Klentaq1), determined at 2.5-A resolution, demonstrates a compact two-domain architecture. The C-terminal domain is identical in fold to the equivalent region of the Klenow fragment of Escherichia coli DNA polymerase I (Klenow pol I). Although the N-terminal domain of Klentaq1 differs greatly in sequence from its counterpart in Klenow pol I, it has clearly evolved from a common ancestor. The structure of Klentaq1 reveals the strategy utilized by this protein to maintain activity at high temperatures and provides the structural basis for future improvements of the enzyme.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20847947

R.G.Federley, and L.J.Romano (2010).
DNA polymerase: structural homology, conformational dynamics, and the effects of carcinogenic DNA adducts.

J Nucleic Acids, 2010, 0.

21123743

S.Obeid, A.Baccaro, W.Welte, K.Diederichs, and A.Marx (2010).
Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase.

Proc Natl Acad Sci U S A, 107, 21327-21331.

PDB codes:

3ojs 3oju

20400942

S.Obeid, N.Blatter, R.Kranaster, A.Schnur, K.Diederichs, W.Welte, and A.Marx (2010).
Replication through an abasic DNA lesion: structural basis for adenine selectivity.

EMBO J, 29, 1738-1747.

PDB codes:

3lwl 3lwm

20080740

Y.Santoso, C.M.Joyce, O.Potapova, L.Le Reste, J.Hohlbein, J.P.Torella, N.D.Grindley, and A.N.Kapanidis (2010).
Conformational transitions in DNA polymerase I revealed by single-molecule FRET.

Proc Natl Acad Sci U S A, 107, 715-720.

20575136

Y.Santoso, J.P.Torella, and A.N.Kapanidis (2010).
Characterizing single-molecule FRET dynamics with probability distribution analysis.

Chemphyschem, 11, 2209-2219.

19778048

D.Loakes, J.Gallego, V.B.Pinheiro, E.T.Kool, and P.Holliger (2009).
Evolving a polymerase for hydrophobic base analogues.

J Am Chem Soc, 131, 14827-14837.

19193992

H.L.Pedersen, N.P.Willassen, and I.Leiros (2009).
The first structure of a cold-adapted superoxide dismutase (SOD): biochemical and structural characterization of iron SOD from Aliivibrio salmonicida.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 84-92.

PDB code:

2w7w

18952180

J.W.Brandis, and K.A.Johnson (2009).
High-cell density shake-flask expression and rapid purification of the large fragment of Thermus aquaticus DNA polymerase I using a new chemically and temperature inducible expression plasmid in Escherichia coli.

Protein Expr Purif, 63, 120-127.

19411253

K.Datta, N.P.Johnson, V.J.LiCata, and P.H.von Hippel (2009).
Local conformations and competitive binding affinities of single- and double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases.

J Biol Chem, 284, 17180-17193.

19208643

M.B.Kermekchiev, L.I.Kirilova, E.E.Vail, and W.M.Barnes (2009).
Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples.

Nucleic Acids Res, 37, e40.

19955412

T.D.Christian, L.J.Romano, and D.Rueda (2009).
Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution.

Proc Natl Acad Sci U S A, 106, 21109-21114.

17939025

D.Wei, and X.Zhang (2008).
Identification and characterization of a single-stranded DNA-binding protein from thermophilic bacteriophage GVE2.

Virus Genes, 36, 273-278.

18287276

W.J.Allen, P.J.Rothwell, and G.Waksman (2008).
An intramolecular FRET system monitors fingers subdomain opening in Klentaq1.

Protein Sci, 17, 401-408.

18025581

M.Khalaj-Kondori, M.Sadeghizadeh, K.Khajeh, H.Naderi-Manesh, A.M.Ahadi, and A.Emamzadeh (2007).
Cloning, sequence analysis and three-dimensional structure prediction of DNA pol I from thermophilic Geobacillus sp. MKK isolated from an Iranian hot spring.

Appl Biochem Biotechnol, 142, 200-208.

17255941

O.Koroleva, N.Makharashvili, C.T.Courcelle, J.Courcelle, and S.Korolev (2007).
Structural conservation of RecF and Rad50: implications for DNA recognition and RecF function.

EMBO J, 26, 867-877.

PDB code:

2o5v

16339886

K.Datta, A.J.Wowor, A.J.Richard, and V.J.LiCata (2006).
Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA.

Biophys J, 90, 1739-1751.

16477622

M.Nayal, and B.Honig (2006).
On the nature of cavities on protein surfaces: application to the identification of drug-binding sites.

Proteins, 63, 892-906.

16802171

P.Filipkowski, A.Duraj-Thatte, and J.Kur (2006).
Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis.

Arch Microbiol, 186, 129-137.

16896528

P.Filipkowski, M.Koziatek, and J.Kur (2006).
A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans.

Extremophiles, 10, 607-614.

16061181

P.J.Rothwell, V.Mitaksov, and G.Waksman (2005).
Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: implications for the molecular basis of fidelity in DNA polymerases.

Mol Cell, 19, 345-355.

16106445

S.Koutsopoulos, J.van der Oost, and W.Norde (2005).
Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering.

Proteins, 61, 377-384.

14997557

A.J.Schoeffler, A.M.Joubert, F.Peng, F.Khan, C.C.Liu, and V.J.LiCata (2004).
Extreme free energy of stabilization of Taq DNA polymerase.

Proteins, 54, 616-621.

15130474

D.Das, and M.M.Georgiadis (2004).
The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus.

Structure, 12, 819-829.

PDB codes:

1rw3 4mh8

15345530

I.Andricioaei, A.Goel, D.Herschbach, and M.Karplus (2004).
Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations.

Biophys J, 87, 1478-1497.

14500822

K.Datta, and V.J.LiCata (2003).
Thermodynamics of the binding of Thermus aquaticus DNA polymerase to primed-template DNA.

Nucleic Acids Res, 31, 5590-5597.

14576300

M.B.Kermekchiev, A.Tzekov, and W.M.Barnes (2003).
Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR.

Nucleic Acids Res, 31, 6139-6147.

11900534

S.Ramón-Maiques, H.G.Britton, and V.Rubio (2002).
Molecular physiology of phosphoryl group transfer from carbamoyl phosphate by a hyperthermophilic enzyme at low temperature.

Biochemistry, 41, 3916-3924.

11453986

B.Clantin, C.Tricot, T.Lonhienne, V.Stalon, and V.Villeret (2001).
Probing the role of oligomerization in the high thermal stability of Pyrococcus furiosus ornithine carbamoyltransferase by site-specific mutants.

Eur J Biochem, 268, 3937-3942.

11264599

C.N.Ji, T.Jiang, M.Q.Chen, X.Y.Sheng, and Y.M.Mao (2001).
Purification, crystallization and preliminary X-ray studies of thermostable alkaline phosphatase from Thermus sp. 3041.

Acta Crystallogr D Biol Crystallogr, 57, 614-615.

11369861

Y.Li, and G.Waksman (2001).
Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: insights into nucleotide incorporation and selectivity.

Protein Sci, 10, 1225-1233.

11090167

H.Liu, J.H.Naismith, and R.T.Hay (2000).
Identification of conserved residues contributing to the activities of adenovirus DNA polymerase.

J Virol, 74, 11681-11689.

11041840

K.Vastmans, S.Pochet, A.Peys, L.Kerremans, A.Van Aerschot, C.Hendrix, P.Marlière, and P.Herdewijn (2000).
Enzymatic incorporation in DNA of 1,5-anhydrohexitol nucleotides.

Biochemistry, 39, 12757-12765.

10966467

T.A.Kunkel, and K.Bebenek (2000).
DNA replication fidelity.

Annu Rev Biochem, 69, 497-529.

10368292

S.Doublié, M.R.Sawaya, and T.Ellenberger (1999).
An open and closed case for all polymerases.

Structure, 7, R31-R35.

10545321

Y.Zhao, D.Jeruzalmi, I.Moarefi, L.Leighton, R.Lasken, and J.Kuriyan (1999).
Crystal structure of an archaebacterial DNA polymerase.

Structure, 7, 1189-1199.

PDB codes:

1d5a 1qqc

9519297

C.A.Brautigam, and T.A.Steitz (1998).
Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.

Curr Opin Struct Biol, 8, 54-63.

9770481

C.Vetriani, D.L.Maeder, N.Tolliday, K.S.Yip, T.J.Stillman, K.L.Britton, D.W.Rice, H.H.Klump, and F.T.Robb (1998).
Protein thermostability above 100 degreesC: a key role for ionic interactions.

Proc Natl Acad Sci U S A, 95, 12300-12305.

10384295

N.A.Woychik (1998).
Fractions to functions: RNA polymerase II thirty years later.

Cold Spring Harb Symp Quant Biol, 63, 311-317.

9770525

R.Murali, D.J.Sharkey, J.L.Daiss, and H.M.Murthy (1998).
Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme.

Proc Natl Acad Sci U S A, 95, 12562-12567.

PDB code:

1bgx

9914251

S.Doublié, and T.Ellenberger (1998).
The mechanism of action of T7 DNA polymerase.

Curr Opin Struct Biol, 8, 704-712.

9485450

W.S.Furey, C.M.Joyce, M.A.Osborne, D.Klenerman, J.A.Peliska, and S.Balasubramanian (1998).
Use of fluorescence resonance energy transfer to investigate the conformation of DNA substrates bound to the Klenow fragment.

Biochemistry, 37, 2979-2990.

9857206

Y.Li, S.Korolev, and G.Waksman (1998).
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

EMBO J, 17, 7514-7525.

PDB codes:

2ktq 3ktq 4ktq

9605316

Y.Li, Y.Kong, S.Korolev, and G.Waksman (1998).
Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.

Protein Sci, 7, 1116-1123.

PDB code:

5ktq

9050827

C.M.Joyce (1997).
Choosing the right sugar: how polymerases select a nucleotide substrate.

Proc Natl Acad Sci U S A, 94, 1619-1622.

9324268

G.C.Fogg, and M.G.Caparon (1997).
Constitutive expression of fibronectin binding in Streptococcus pyogenes as a result of anaerobic activation of rofA.

J Bacteriol, 179, 6172-6180.

9016716

J.R.Kiefer, C.Mao, C.J.Hansen, S.L.Basehore, H.H.Hogrefe, J.C.Braman, and L.S.Beese (1997).
Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.

Structure, 5, 95.

PDB codes:

1bdp 1xwl

9215631

J.Wang, A.K.Sattar, C.C.Wang, J.D.Karam, W.H.Konigsberg, and T.A.Steitz (1997).
Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.

Cell, 89, 1087-1099.

PDB codes:

1waf 1wag 1wah 1wai 1waj

9013648

T.D.Yager, J.M.Dunn, and J.K.Stevens (1997).
High-speed DNA sequencing in ultrathin slab gels.

Curr Opin Biotechnol, 8, 107-113.

8665867

G.Martin, and W.Keller (1996).
Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases.

EMBO J, 15, 2593-2603.

8710517

J.M.Hite, K.A.Eckert, and K.C.Cheng (1996).
Factors affecting fidelity of DNA synthesis during PCR amplification of d(C-A)n.d(G-T)n microsatellite repeats.

Nucleic Acids Res, 24, 2429-2434.

8646784

K.K.Leuther, D.A.Bushnell, and R.D.Kornberg (1996).
Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation.

Cell, 85, 773-779.

8790389

M.Suzuki, D.Baskin, L.Hood, and L.A.Loeb (1996).
Random mutagenesis of Thermus aquaticus DNA polymerase I: concordance of immutable sites in vivo with the crystal structure.

Proc Natl Acad Sci U S A, 93, 9670-9675.

9238641

M.Suzuki, F.C.Christians, B.Kim, A.Skandalis, M.E.Black, and L.A.Loeb (1996).
Tolerance of different proteins for amino acid diversity.

Mol Divers, 2, 111-118.

8627740

S.H.Hughes, Z.Hostomsky, S.F.Le Grice, K.Lentz, and E.Arnold (1996).
What is the orientation of DNA polymerases on their templates?

J Virol, 70, 2679-2683.

8954159

T.Hermann, and H.Heumann (1996).
Strained template under the thumbs. How reverse transcriptase of human immunodeficiency virus type 1 moves along its template.

Eur J Biochem, 242, 98.

8762133

T.Salminen, A.Teplyakov, J.Kankare, B.S.Cooperman, R.Lahti, and A.Goldman (1996).
An unusual route to thermostability disclosed by the comparison of Thermus thermophilus and Escherichia coli inorganic pyrophosphatases.

Protein Sci, 5, 1014-1025.

8747452

A.Goldman (1995).
How to make my blood boil.

Structure, 3, 1277-1279.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.