2IDO | pdb_00002ido

Structure of the E. coli Pol III epsilon-Hot proofreading complex

PDB DOI: https://doi.org/10.2210/pdb2IDO/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli, Punavirus P1
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2006-09-15 Released: 2006-11-14
Deposition Author(s): Kirby, T.W., Harvey, S., DeRose, E.F., Chalov, S., Chikova, A.K., Perrino, F.W., Schaaper, R.M., London, R.E., Pedersen, L.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.244 (Depositor), 0.247 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex.

Kirby, T.W., Harvey, S., DeRose, E.F., Chalov, S., Chikova, A.K., Perrino, F.W., Schaaper, R.M., London, R.E., Pedersen, L.C.

(2006) J Biological Chem 281: 38466-38471

PubMed: 16973612 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M606917200
Primary Citation Related Structures:
2IDO

PubMed Abstract:
The epsilon subunit of Escherichia coli DNA polymerase III possesses 3'-exonucleolytic proofreading activity. Within the Pol III core, epsilon is tightly bound between the alpha subunit (DNA polymerase) and subunit. Here, we present the crystal structure of epsilon in complex with HOT, the bacteriophage P1-encoded homolog of , at 2.1 A resolution. The epsilon-HOT interface is defined by two areas of contact: an interaction of the previously unstructured N terminus of HOT with an edge of the epsilon central beta-sheet as well as interactions between HOT and the catalytically important helix alpha1-loop-helix alpha2 motif of epsilon. This structure provides insight into how HOT and, by implication, may stabilize the epsilon subunit, thus promoting efficient proofreading during chromosomal replication.

Organizational Affiliation

Laboratory of Structural Biology, National Institute of Environmental Health Sciences/NIH, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA.

Macromolecule Content

Total Structure Weight: 61.88 kDa
Atom Count: 4,450
Modeled Residue Count: 499
Deposited Residue Count: 538
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III epsilon subunit	A, C	186	Escherichia coli	Mutation(s): 0 Gene Names: dnaQ, mutD EC: 2.7.7.7
UniProt
Find proteins for P03007 (Escherichia coli (strain K12)) Explore P03007 Go to UniProtKB: P03007
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03007
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hot protein	B, D	83	Punavirus P1	Mutation(s): 0 Gene Names: hot
UniProt
Find proteins for Q71T70 (Escherichia phage P1) Explore Q71T70 Go to UniProtKB: Q71T70
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q71T70
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TMP Query on TMP Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A]	G [auth A], K [auth C]	THYMIDINE-5'-PHOSPHATE C₁₀ H₁₅ N₂ O₈ P GYOZYWVXFNDGLU-XLPZGREQSA-N		Interactions Focus chain G [auth A] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth C] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth C], I [auth C], J [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.244 (Depositor), 0.247 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.209 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.289	α = 90
b = 77.289	β = 90
c = 212.978	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description