3SYZ

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase

PDB DOI: https://doi.org/10.2210/pdb3SYZ/pdb
NAKB: 3SYZ

Classification: TRANSFERASE/DNA
Organism(s): Thermus aquaticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-07-18 Released: 2012-06-06
Deposition Author(s): Betz, K., Diederichs, K., Marx, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 ?
R-Value Free: 0.201
R-Value Work: 0.160
R-Value Observed: 0.162

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Dwyer, T.J., Ordoukhanian, P., Romesberg, F.E., Marx, A.

(2012) Nat Chem Biol 8: 612-614

PubMed: 22660438 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nchembio.966
Primary Citation of Related Structures:
3RTV, 3SV3, 3SV4, 3SYZ, 3SZ2

PubMed Abstract:
Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

Organizational Affiliation

Department of Chemistry, Universit?t Konstanz, Konstanz, Germany.

Macromolecule Content

Total Structure Weight: 70.77 kDa
Atom Count: 5,305
Modelled Residue Count: 568
Deposited Residue Count: 568
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase I, thermostable	A	540	Thermus aquaticus	Mutation(s): 0 Gene Names: pol I, pol1, polA EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus) Explore P19821 Go to UniProtKB: P19821
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19821
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
(5'-D(GPAPCPCPAPCPGPGPCPGPCP(DOC))-3')	B	12	N/A
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
(5'-D(APAPAP(BMN)PGPGPCPGPCPCPGPTPGPGPTPC)-3')	C	16	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], N [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B]	O [auth A], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 ?
R-Value Free: 0.201
R-Value Work: 0.160
R-Value Observed: 0.162
Space Group: P 3₁ 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 108.529	α = 90
b = 108.529	β = 90
c = 90.524	γ = 120

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Betz, K.

Diederichs, K.

Marx, A.

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2012-07-04
Changes: Database references
Version 1.2: 2012-09-12
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3SYZ

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Sequence Annotations

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Entity ID: 3

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)