PDBsum entry 2axd

Transferase

PDB id

2axd

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Contents

			Protein chain

					76 a.a. *

* Residue conservation analysis

PDB id:

2axd

Links
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- ProSAT

Name:

Transferase

Title:

Solution structure of the theta subunit of escherichia coli DNA polymerase iii in complex with the epsilon subunit

Structure:

DNA polymerase iii, theta subunit. Chain: s. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: hole. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

12 models

Authors:

M.A.Keniry,A.Y.Park,E.A.Owen,S.M.Hamdan,G.Pintacuda,G.Otting, N.E.Dixon

Key ref:

M.A.Keniry et al. (2006). Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit. J Bacteriol, 188, 4464-4473. PubMed id: 16740953

Date:

05-Sep-05

Release date:

04-Jul-06

PROCHECK

	Headers

	References

Protein chain

P0ABS8 (HOLE_ECOLI) - DNA polymerase III subunit theta from Escherichia coli (strain K12)

Seq: Struc:					76 a.a. 76 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

	J Bacteriol 188:4464-4473 (2006)
PubMed id: 16740953

Structure of the theta subunit of Escherichia coli DNA polymerase III in complex with the epsilon subunit.
M.A.Keniry, A.Y.Park, E.A.Owen, S.M.Hamdan, G.Pintacuda, G.Otting, N.E.Dixon.

ABSTRACT

The catalytic core of Escherichia coli DNA polymerase III contains three tightly associated subunits, the alpha, epsilon, and theta subunits. The theta subunit is the smallest and least understood subunit. The three-dimensional structure of theta in a complex with the unlabeled N-terminal domain of the epsilon subunit, epsilon186, was determined by multidimensional nuclear magnetic resonance spectroscopy. The structure was refined using pseudocontact shifts that resulted from inserting a lanthanide ion (Dy3+, Er3+, or Ho3+) at the active site of epsilon186. The structure determination revealed a three-helix bundle fold that is similar to the solution structures of theta in a methanol-water buffer and of the bacteriophage P1 homolog, HOT, in aqueous buffer. Conserved nuclear Overhauser enhancement (NOE) patterns obtained for free and complexed theta show that most of the structure changes little upon complex formation. Discrepancies with respect to a previously published structure of free theta (Keniry et al., Protein Sci. 9:721-733, 2000) were attributed to errors in the latter structure. The present structure satisfies the pseudocontact shifts better than either the structure of theta in methanol-water buffer or the structure of HOT. satisfies these shifts. The epitope of epsilon186 on theta was mapped by NOE difference spectroscopy and was found to involve helix 1 and the C-terminal part of helix 3. The pseudocontact shifts indicated that the helices of theta are located about 15 A or farther from the lanthanide ion in the active site of epsilon186, in agreement with the extensive biochemical data for the theta-epsilon system.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21417597

A.Y.Park, and C.V.Robinson (2011).
Protein-nucleic acid complexes and the role of mass spectrometry in their structure determination.

Crit Rev Biochem Mol Biol, 46, 152-164.

20462377

G.Otting (2010).
Protein NMR using paramagnetic ions.

Annu Rev Biophys, 39, 387-405.

19651049

J.Batra, K.Xu, S.Qin, and H.X.Zhou (2009).
Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences.

Biophys J, 97, 906-911.

18574699

C.Schmitz, M.J.Stanton-Cook, X.C.Su, G.Otting, and T.Huber (2008).
Numbat: an interactive software tool for fitting Deltachi-tensors to molecular coordinates using pseudocontact shifts.

J Biomol NMR, 41, 179-189.

18663010

K.Ozawa, S.Jergic, A.Y.Park, N.E.Dixon, and G.Otting (2008).
The proofreading exonuclease subunit epsilon of Escherichia coli DNA polymerase III is tethered to the polymerase subunit alpha via a flexible linker.

Nucleic Acids Res, 36, 5074-5082.

17096205

M.John, M.J.Headlam, N.E.Dixon, and G.Otting (2007).
Assignment of paramagnetic (15)N-HSQC spectra by heteronuclear exchange spectroscopy.

J Biomol NMR, 37, 43-51.

16973612

T.W.Kirby, S.Harvey, E.F.DeRose, S.Chalov, A.K.Chikova, F.W.Perrino, R.M.Schaaper, R.E.London, and L.C.Pedersen (2006).
Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex.

J Biol Chem, 281, 38466-38471.

PDB code:

2ido

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.