PDBsum entry 1wns

Transferase

PDB id

1wns

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Contents

			Protein chain

					729 a.a. *

* Residue conservation analysis

PDB id:

1wns

Links

Name:

Transferase

Title:

Crystal structure of family b DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis kod1

Structure:

DNA polymerase. Chain: a. Engineered: yes

Source:

Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.00Å

R-factor:

0.231

R-free:

0.313

Authors:

H.Hashimoto,T.Inoue,Y.Kai,S.Fujiwara,M.Takagi,M.Nishioka,T.Imanaka

Key ref:

H.Hashimoto et al. (2001). Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. J Mol Biol, 306, 469-477. PubMed id: 11178906 DOI: 10.1006/jmbi.2000.4403

Date:

09-Aug-04

Release date:

17-Aug-04

Supersedes:

1gcx

PROCHECK

	Headers

	References

Protein chain

P77933 (DPOL_THEKO) - DNA polymerase from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: Struc:

Seq: Struc:

Seq: Struc:

Seq: Struc:					1671 a.a. 729 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class 2:

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

Enzyme class 3:

E.C.3.1.-.-

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

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1006/jmbi.2000.4403	J Mol Biol 306:469-477 (2001)
PubMed id: 11178906

Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
H.Hashimoto, M.Nishioka, S.Fujiwara, M.Takagi, T.Imanaka, T.Inoue, Y.Kai.

ABSTRACT

The crystal structure of family B DNA polymerase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 (KOD DNA polymerase) was determined. KOD DNA polymerase exhibits the highest known extension rate, processivity and fidelity. We carried out the structural analysis of KOD DNA polymerase in order to clarify the mechanisms of those enzymatic features. Structural comparison of DNA polymerases from hyperthermophilic archaea highlighted the conformational difference in Thumb domains. The Thumb domain of KOD DNA polymerase shows an "opened" conformation. The fingers subdomain possessed many basic residues at the side of the polymerase active site. The residues are considered to be accessible to the incoming dNTP by electrostatic interaction. A beta-hairpin motif (residues 242-249) extends from the Exonuclease (Exo) domain as seen in the editing complex of the RB69 DNA polymerase from bacteriophage RB69. Many arginine residues are located at the forked-point (the junction of the template-binding and editing clefts) of KOD DNA polymerase, suggesting that the basic environment is suitable for partitioning of the primer and template DNA duplex and for stabilizing the partially melted DNA structure in the high-temperature environments. The stabilization of the melted DNA structure at the forked-point may be correlated with the high PCR performance of KOD DNA polymerase, which is due to low error rate, high elongation rate and processivity.

Selected figure(s)



	Figure 1. Figure 1. (a) Overall structure of KOD DNA polymerase. The struc- ture is composed of domains and subdomains, which are N-terminal (N-ter, violet), Exonuclease (Exo, blue), Polymerase (Pol) domain including the Palm (brown) and Fingers (green) subdomains and the Thumb domain (red), including the Thumb-1 and Thumb-2 subdo- mains. Conserved carboxylate residues in Polymerase and Exonu- clease active site are shown by ball- and-stick models. (b) Confor- mational comparison of Thumb domains among three archaeal DNA polymerases. Red, KOD DNA polymerase; blue, Tgo DNA polymerase; and green, 9°N-7 DNA polymerase. The comparison shows that the Thumb domain of KOD DNA polymerase displays the most ``opened'' conformation.		Figure 4. Figure 4. Molecular surface with electrostatic potential map around the forked-point. The red and blue surfaces are acidic and basic regions, respectively. Domains and subdomains are labeled with orange letters. Polymerase and Exonuclease active sites are labeled with P and E, respectively. The b-hairpin is labeled with b.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21062827

C.J.Hansen, L.Wu, J.D.Fox, B.Arezi, and H.H.Hogrefe (2011).
Engineered split in Pfu DNA polymerase fingers domain improves incorporation of nucleotide gamma-phosphate derivative.

Nucleic Acids Res, 39, 1801-1810.

21245343

K.Mayanagi, S.Kiyonari, H.Nishida, M.Saito, D.Kohda, Y.Ishino, T.Shirai, and K.Morikawa (2011).
Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex.

Proc Natl Acad Sci U S A, 108, 1845-1849.

20163964

E.Johansson, and S.A.Macneill (2010).
The eukaryotic replicative DNA polymerases take shape.

Trends Biochem Sci, 35, 339-347.

19947980

I.del Olmo, L.López-González, M.M.Martín-Trillo, J.M.Martínez-Zapater, M.Piñeiro, and J.A.Jarillo (2010).
EARLY IN SHORT DAYS 7 (ESD7) encodes the catalytic subunit of DNA polymerase epsilon and is required for flowering repression through a mechanism involving epigenetic gene silencing.

Plant J, 61, 623-636.

20851826

J.G.Song, E.J.Kil, S.S.Cho, I.H.Kim, and S.T.Kwon (2010).
An amino acid residue in the middle of the fingers subdomain is involved in Neq DNA polymerase processivity: enhanced processivity of engineered Neq DNA polymerase and its PCR application.

Protein Eng Des Sel, 23, 835-842.

19420796

H.Matsukawa, T.Yamagami, Y.Kawarabayasi, Y.Miyashita, M.Takahashi, and Y.Ishino (2009).
A useful strategy to construct DNA polymerases with different properties by using genetic resources from environmental DNA.

Genes Genet Syst, 84, 3.

19033368

I.Rodríguez, J.M.Lázaro, M.Salas, and M.de Vega (2009).
Involvement of the TPR2 subdomain movement in the activities of phi29 DNA polymerase.

Nucleic Acids Res, 37, 193-203.

19300826

R.N.Veedu, B.Vester, and J.Wengel (2009).
Efficient enzymatic synthesis of LNA-modified DNA duplexes using KOD DNA polymerase.

Org Biomol Chem, 7, 1404-1409.

18583360

M.Kuwahara, S.Obika, J.Nagashima, Y.Ohta, Y.Suto, H.Ozaki, H.Sawai, and T.Imanishi (2008).
Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides.

Nucleic Acids Res, 36, 4257-4265.

18606739

R.Raghavan, L.D.Hicks, and M.F.Minnick (2008).
Toxic introns and parasitic intein in Coxiella burnetii: legacies of a promiscuous past.

J Bacteriol, 190, 5934-5943.

17988102

A.P.Silverman, Q.Jiang, M.F.Goodman, and E.T.Kool (2007).
Steric and electrostatic effects in DNA synthesis by the SOS-induced DNA polymerases II and IV of Escherichia coli.

Biochemistry, 46, 13874-13881.

17098747

M.Hogg, P.Aller, W.Konigsberg, S.S.Wallace, and S.Doublié (2007).
Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family.

J Biol Chem, 282, 1432-1444.

PDB code:

2dtu

17012278

M.Kuwahara, J.Nagashima, M.Hasegawa, T.Tamura, R.Kitagata, K.Hanawa, S.Hososhima, T.Kasamatsu, H.Ozaki, and H.Sawai (2006).
Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA.

Nucleic Acids Res, 34, 5383-5394.

16705640

R.Shi, A.Azzi, C.Gilbert, G.Boivin, and S.X.Lin (2006).
Three-dimensional modeling of cytomegalovirus DNA polymerase and preliminary analysis of drug resistance.

Proteins, 64, 301-307.

15707490

H.Ogata, D.Raoult, and J.M.Claverie (2005).
A new example of viral intein in Mimivirus.

Virol J, 2, 8.

15845765

I.Rodríguez, J.M.Lázaro, L.Blanco, S.Kamtekar, A.J.Berman, J.Wang, T.A.Steitz, M.Salas, and M.de Vega (2005).
A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity.

Proc Natl Acad Sci U S A, 102, 6407-6412.

16257257

K.Egorova, and G.Antranikian (2005).
Industrial relevance of thermophilic Archaea.

Curr Opin Microbiol, 8, 649-655.

15976864

T.Ohbayashi, M.Kuwahara, M.Hasegawa, T.Kasamatsu, T.Tamura, and H.Sawai (2005).
Expansion of repertoire of modified DNAs prepared by PCR using KOD Dash DNA polymerase.

Org Biomol Chem, 3, 2463-2468.

14699133

A.F.Gardner, C.M.Joyce, and W.E.Jack (2004).
Comparative kinetics of nucleotide analog incorporation by vent DNA polymerase.

J Biol Chem, 279, 11834-11842.

15109812

A.R.Pavlov, N.V.Pavlova, S.A.Kozyavkin, and A.I.Slesarev (2004).
Recent developments in the optimization of thermostable DNA polymerases for efficient applications.

Trends Biotechnol, 22, 253-260.

15601989

B.D.Biles, and B.A.Connolly (2004).
Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR.

Nucleic Acids Res, 32, e176.

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

15057282

E.Freisinger, A.P.Grollman, H.Miller, and C.Kisker (2004).
Lesion (in)tolerance reveals insights into DNA replication fidelity.

EMBO J, 23, 1494-1505.

PDB codes:

1q9x 1q9y

15057283

M.Hogg, S.S.Wallace, and S.Doublié (2004).
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.

EMBO J, 23, 1483-1493.

PDB codes:

1rv2 2p5o

14729920

V.Truniger, J.M.Lázaro, and M.Salas (2004).
Function of the C-terminus of phi29 DNA polymerase in DNA and terminal protein binding.

Nucleic Acids Res, 32, 361-370.

14694096

Y.T.Hwang, H.J.Zuccola, Q.Lu, and C.B.Hwang (2004).
A point mutation within conserved region VI of herpes simplex virus type 1 DNA polymerase confers altered drug sensitivity and enhances replication fidelity.

J Virol, 78, 650-657.

14527289

B.Grabowski, and Z.Kelman (2003).
Archeal DNA replication: eukaryal proteins in a bacterial context.

Annu Rev Microbiol, 57, 487-516.

12591889

T.Kanai, S.Ito, and T.Imanaka (2003).
Characterization of a cytosolic NiFe-hydrogenase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.

J Bacteriol, 185, 1705-1711.

16233341

H.Atomi (2002).
Microbial enzymes involved in carbon dioxide fixation.

J Biosci Bioeng, 94, 497-505.

12415291

M.J.Fogg, L.H.Pearl, and B.A.Connolly (2002).
Structural basis for uracil recognition by archaeal family B DNA polymerases.

Nat Struct Biol, 9, 922-927.

12450132

M.Kitabayashi, Y.Nishiya, M.Esaka, M.Itakura, and T.Imanaka (2002).
Gene cloning and polymerase chain reaction with proliferating cell nuclear antigen from Thermococcus kodakaraensis KOD1.

Biosci Biotechnol Biochem, 66, 2194-2200.

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.

12057965

T.Fukui, T.Eguchi, H.Atomi, and T.Imanaka (2002).
A membrane-bound archaeal Lon protease displays ATP-independent proteolytic activity towards unfolded proteins and ATP-dependent activity for folded proteins.

J Bacteriol, 184, 3689-3698.

12112867

T.Imanaka, and H.Atomi (2002).
Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea.

Chem Rec, 2, 149-163.

11917008

V.Truniger, J.M.Lázaro, F.J.Esteban, L.Blanco, and M.Salas (2002).
A positively charged residue of phi29 DNA polymerase, highly conserved in DNA polymerases from families A and B, is involved in binding the incoming nucleotide.

Nucleic Acids Res, 30, 1483-1492.

11526322

I.D.Kerr, R.I.Wadsworth, W.Blankenfeldt, A.G.Staines, M.F.White, and J.H.Naismith (2001).
Overexpression, purification, crystallization and data collection of a single-stranded DNA-binding protein from Sulfolobus solfataricus.

Acta Crystallogr D Biol Crystallogr, 57, 1290-1292.

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 code is shown on the right.