PDBsum entry 1xwl

DNA replication

PDB id

1xwl

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Contents

			Protein chain

					580 a.a. *

			Ligands

					SO4 ×2

			Waters ×405

* Residue conservation analysis

PDB id:

1xwl

Links

Name:

DNA replication

Title:

Bacillus stearothermophilus (newly identified strain as yet unnamed) DNA polymerase fragment

Structure:

DNA polymerase i. Chain: a. Fragment: residues 297-876. Synonym: bf. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: bacillus stearothermophilus. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å

R-factor:

0.254

R-free:

0.291

Authors:

J.R.Kiefer,C.Mao,L.S.Beese

Key ref:

J.R.Kiefer et al. (1997). Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution. Structure, 5, 95. PubMed id: 9016716 DOI: 10.1016/S0969-2126(97)00169-X

Date:

22-Jul-98

Release date:

13-Jan-99

Supersedes:

1bdp

PROCHECK

	Headers

	References

Protein chain

P52026 (DPO1_GEOSE) - DNA polymerase I from Geobacillus stearothermophilus

Seq: Struc:

Seq: Struc:					876 a.a. 580 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 67 residue positions (black crosses)



		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: 10.1016/S0969-2126(97)00169-X	Structure 5:95 (1997)
PubMed id: 9016716

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

ABSTRACT

BACKGROUND: The study of DNA polymerases in the Pol l family is central to the understanding of DNA replication and repair. DNA polymerases are used in many molecular biology techniques, including PCR, which require a thermostable polymerase. In order to learn about Pol I function and the basis of thermostability, we undertook structural studies of a new thermostable DNA polymerase. RESULTS: A DNA polymerase large, Klenow-like, fragment from a recently identified thermostable strain of Bacillus stearothermophilus (BF) was cloned, sequenced, overexpressed and characterized. Its crystal structure was determined to 2.1 A resolution by the method of multiple isomorphous replacement. CONCLUSIONS: This structure represents the highest resolution view of a Pol I enzyme obtained to date. Comparison of the three Pol I structures reveals no compelling evidence for many of the specific interactions that have been proposed to induce thermostability, but suggests that thermostability arises from innumerable small changes distributed throughout the protein structure. The polymerase domain is highly conserved in all three proteins. The N-terminal domains are highly divergent in sequence, but retain a common fold. When present, the 3'-5' proofreading exonuclease activity is associated with this domain. Its absence is associated with changes in catalytic residues that coordinate the divalent ions required for activity and in loops connecting homologous secondary structural elements. In BF, these changes result in a blockage of the DNA-binding cleft.

Selected figure(s)



	Figure 3. Figure 3. Comparison of 3'-5' exonuclease active sites. Stereo diagram of the BF polymerase vestigial exonuclease active site (red) with the position of a portion of the structure of the KF active site (gold) [4] superimposed. The KF Ca backbone schematic is accompanied by is two bound zinc atoms (green), and three nucleotides (black) from the KF editing complex [11]. The KF residues shown (yellow) are the four residues that bind the two metal ions essential for catalysis. These essential KF sidechains Asp355, Glu357, Asp424, and Asp501 correspond to BF residues Val319, Glu321, Ala376, and Lys450, respectively (shown in blue). Also shown in blue are two BF proline residues (438 and 441) that may be responsible for the collapse of a loop between helices E[1] and F (dotted line) into the exonuclease cleft not observed in KF. (Drawn with RIBBONS [71].)

Figure was selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20152155

A.A.Golosov, J.J.Warren, L.S.Beese, and M.Karplus (2010).
The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.

Structure, 18, 83-93.

PDB codes:

3eyz 3ez5

20813757

M.Münzel, L.Lercher, M.Müller, and T.Carell (2010).
Chemical discrimination between dC and 5MedC via their hydroxylamine adducts.

Nucleic Acids Res, 38, e192.

PDB code:

2xo7

20057044

V.B.Chen, W.B.Arendall, J.J.Headd, D.A.Keedy, R.M.Immormino, G.J.Kapral, L.W.Murray, J.S.Richardson, and D.C.Richardson (2010).
MolProbity: all-atom structure validation for macromolecular crystallography.

Acta Crystallogr D Biol Crystallogr, 66, 12-21.

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.

19276069

M.Horiuchi, K.Takeuchi, N.Noda, N.Muroya, T.Suzuki, T.Nakamura, J.Kawamura-Tsuzuku, K.Takahasi, T.Yamamoto, and F.Inagaki (2009).
Structural Basis for the Antiproliferative Activity of the Tob-hCaf1 Complex.

J Biol Chem, 284, 13244-13255.

PDB code:

2d5r

19348507

M.Trostler, A.Delier, J.Beckman, M.Urban, J.N.Patro, T.E.Spratt, L.S.Beese, and R.D.Kuchta (2009).
Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus.

Biochemistry, 48, 4633-4641.

19364137

P.Xu, L.Oum, Y.C.Lee, N.E.Geacintov, and S.Broyde (2009).
Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase.

Biochemistry, 48, 4677-4690.

18217762

A.M.Leconte, G.T.Hwang, S.Matsuda, P.Capek, Y.Hari, and F.E.Romesberg (2008).
Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet.

J Am Chem Soc, 130, 2336-2343.

18058909

R.Venkatramani, and R.Radhakrishnan (2008).
Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus.

Proteins, 71, 1360-1372.

18407502

S.Broyde, L.Wang, O.Rechkoblit, N.E.Geacintov, and D.J.Patel (2008).
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases.

Trends Biochem Sci, 33, 209-219.

17118716

M.E.Arana, K.Takata, M.Garcia-Diaz, R.D.Wood, and T.A.Kunkel (2007).
A unique error signature for human DNA polymerase nu.

DNA Repair (Amst), 6, 213-223.

18496613

M.Garcia-Diaz, and K.Bebenek (2007).
Multiple functions of DNA polymerases.

CRC Crit Rev Plant Sci, 26, 105-122.

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.

17576677

P.Xu, L.Oum, L.S.Beese, N.E.Geacintov, and S.Broyde (2007).
Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.

Nucleic Acids Res, 35, 4275-4288.

16045613

S.Duigou, S.D.Ehrlich, P.Noirot, and M.F.Noirot-Gros (2005).
DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis.

Mol Microbiol, 57, 678-690.

15322558

G.W.Hsu, M.Ober, T.Carell, and L.S.Beese (2004).
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase.

Nature, 431, 217-221.

PDB codes:

1u45 1u47 1u48 1u49 1u4b

15211513

L.L.Videau, W.B.Arendall, and J.S.Richardson (2004).
The cis-Pro touch-turn: a rare motif preferred at functional sites.

Proteins, 56, 298-309.

15035983

S.J.Johnson, and L.S.Beese (2004).
Structures of mismatch replication errors observed in a DNA polymerase.

Cell, 116, 803-816.

PDB codes:

1njw 1njx 1njy 1njz 1nk0 1nk4 1nk5 1nk6 1nk7 1nk8 1nk9 1nkb 1nkc 1nke

14704353

Y.Shen, X.F.Tang, H.Yokoyama, E.Matsui, and I.Matsui (2004).
A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor.

Nucleic Acids Res, 32, 158-168.

12522214

K.Singh, and M.J.Modak (2003).
Presence of 18-A long hydrogen bond track in the active site of Escherichia coli DNA polymerase I (Klenow fragment). Its requirement in the stabilization of enzyme-template-primer complex.

J Biol Chem, 278, 11289-11302.

12649320

S.J.Johnson, J.S.Taylor, and L.S.Beese (2003).
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.

Proc Natl Acad Sci U S A, 100, 3895-3900.

PDB codes:

1l3s 1l3t 1l3u 1l3v 1l5u 1lv5

11884636

R.Eisenbrandt, J.M.Lázaro, M.Salas, and M.de Vega (2002).
Phi29 DNA polymerase residues Tyr59, His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein.

Nucleic Acids Res, 30, 1379-1386.

12364611

S.W.Yang, M.Astatke, J.Potter, and D.K.Chatterjee (2002).
Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides.

Nucleic Acids Res, 30, 4314-4320.

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.

11050188

K.Chowdhury, S.Tabor, and C.C.Richardson (2000).
A unique loop in the DNA-binding crevice of bacteriophage T7 DNA polymerase influences primer utilization.

Proc Natl Acad Sci U S A, 97, 12469-12474.

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.

10666444

S.J.Evans, M.J.Fogg, A.Mamone, M.Davis, L.H.Pearl, and B.A.Connolly (2000).
Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from the archaeon Pyrococcus furiosus.

Nucleic Acids Res, 28, 1059-1066.

10966467

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

Annu Rev Biochem, 69, 497-529.

10595540

G.Martin, P.Jenö, and W.Keller (1999).
Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.

Protein Sci, 8, 2380-2391.

10047577

J.Jäger, and J.D.Pata (1999).
Getting a grip: polymerases and their substrate complexes.

Curr Opin Struct Biol, 9, 21-28.

10097083

K.P.Hopfner, A.Eichinger, R.A.Engh, F.Laue, W.Ankenbauer, R.Huber, and B.Angerer (1999).
Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.

Proc Natl Acad Sci U S A, 96, 3600-3605.

PDB code:

1tgo

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.

9826686

I.K.Cann, K.Komori, H.Toh, S.Kanai, and Y.Ishino (1998).
A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase.

Proc Natl Acad Sci U S A, 95, 14250-14255.

9849940

J.Sanz-Aparicio, J.A.Hermoso, M.Martínez-Ripoll, B.González, C.López-Camacho, and J.Polaina (1998).
Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of beta-glucosidase A from Bacillus polymyxa.

Proteins, 33, 567-576.

PDB code:

1e4i

9786901

M.de Vega, L.Blanco, and M.Salas (1998).
phi29 DNA polymerase residue Ser122, a single-stranded DNA ligand for 3'-5' exonucleolysis, is required to interact with the terminal protein.

J Biol Chem, 273, 28966-28977.

9914251

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

Curr Opin Struct Biol, 8, 704-712.

9461069

T.A.Kunkel, and S.H.Wilson (1998).
DNA polymerases on the move.

Nat Struct Biol, 5, 95-99.

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.

10333564

Y.Ishino, and I.K.Cann (1998).
The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: fact or farce?

Genes Genet Syst, 73, 323-336.

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

9388236

M.Oliveros, R.J.Yáñez, M.L.Salas, J.Salas, E.Viñuela, and L.Blanco (1997).
Characterization of an African swine fever virus 20-kDa DNA polymerase involved in DNA repair.

J Biol Chem, 272, 30899-30910.

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.