PDBsum entry 2vye

Hydrolase/DNA

PDB id

2vye

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Contents

			Protein chains

					425 a.a. *


					381 a.a. *

			DNA/RNA

* Residue conservation analysis

PDB id:

2vye

Links

Name:

Hydrolase/DNA

Title:

Crystal structure of the dnac-ssdna complex

Structure:

Replicative DNA helicase. Chain: a, b. Synonym: dnac. Engineered: yes. 5'-d( Tp Tp Tp Tp Tp Tp Tp Tp Tp)-3'. Chain: c. Synonym: ssdt15. Engineered: yes

Source:

Geobacillus kaustophilus hta426. Organism_taxid: 235909. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Escherichia coli. Organism_taxid: 562

Resolution:

4.10Å

R-factor:

0.302

R-free:

0.374

Authors:

Y.H.Lo,K.L.Tsai,Y.J.Sun,C.D.Hsiao

Key ref:

Y.H.Lo et al. (2009). The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA. Nucleic Acids Res, 37, 804-814. PubMed id: 19074952

Date:

23-Jul-08

Release date:

30-Dec-08

PROCHECK

	Headers

	References

Protein chain

Q5KU75 (Q5KU75_GEOKA) - Replicative DNA helicase from Geobacillus kaustophilus (strain HTA426)

Seq: Struc:					454 a.a. 425 a.a.

Protein chain

Q5KU75 (Q5KU75_GEOKA) - Replicative DNA helicase from Geobacillus kaustophilus (strain HTA426)

Seq: Struc:					454 a.a. 381 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

DNA/RNA chain

T-T-T-T-T-T-T-T-T 9 bases



		Enzyme reactions

Enzyme class:

Chains A, B: E.C.3.6.4.12 - Dna helicase.

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

Reaction:

ATP + H2O = ADP + phosphate + H⁺

ATP	+	H2O	=	ADP	+	phosphate	+	H(+)

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

reference

	Nucleic Acids Res 37:804-814 (2009)
PubMed id: 19074952

The crystal structure of a replicative hexameric helicase DnaC and its complex with single-stranded DNA.
Y.H.Lo, K.L.Tsai, Y.J.Sun, W.T.Chen, C.Y.Huang, C.D.Hsiao.

ABSTRACT

DNA helicases are motor proteins that play essential roles in DNA replication, repair and recombination. In the replicative hexameric helicase, the fundamental reaction is the unwinding of duplex DNA; however, our understanding of this function remains vague due to insufficient structural information. Here, we report two crystal structures of the DnaB-family replicative helicase from Geobacillus kaustophilus HTA426 (GkDnaC) in the apo-form and bound to single-stranded DNA (ssDNA). The GkDnaC-ssDNA complex structure reveals that three symmetrical basic grooves on the interior surface of the hexamer individually encircle ssDNA. The ssDNA-binding pockets in this structure are directed toward the N-terminal domain collar of the hexameric ring, thus orienting the ssDNA toward the DnaG primase to facilitate the synthesis of short RNA primers. These findings provide insight into the mechanism of ssDNA binding and provide a working model to establish a novel mechanism for DNA translocation at the replication fork.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21210194

C.C.Chen, and C.Y.Huang (2011).
Inhibition of Klebsiella pneumoniae DnaB helicase by the flavonol galangin.

Protein J, 30, 59-65.

20129058

M.Makowska-Grzyska, and J.M.Kaguni (2010).
Primase directs the release of DnaC from DnaB.

Mol Cell, 37, 90.

19255093

K.V.Loscha, K.Jaudzems, C.Ioannou, X.C.Su, F.R.Hill, G.Otting, N.E.Dixon, and E.Liepinsh (2009).
A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader.

Nucleic Acids Res, 37, 2395-2404.

PDB code:

2k7r

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.