2PYJ | pdb_00002pyj

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)

PDB DOI: https://doi.org/10.2210/pdb2PYJ/pdb
NAKB: 2PYJ

Classification: REPLICATION, TRANSFERASE/DNA
Organism(s): Salasvirus phi29
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-16 Released: 2007-07-17
Deposition Author(s): Berman, A.J., Kamtekar, S., Goodman, J.L., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.234 (Depositor), 0.284 (DCC)
R-Value Work:
0.189 (Depositor), 0.245 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases

Berman, A.J., Kamtekar, S., Goodman, J.L., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

(2007) EMBO J 26: 3494-3505

PubMed: 17611604 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/sj.emboj.7601780
Primary Citation Related Structures:
2PY5, 2PYJ, 2PYL, 2PZS

PubMed Abstract:
Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Macromolecule Content

Total Structure Weight: 158.99 kDa
Atom Count: 11,997
Modeled Residue Count: 1,210
Deposited Residue Count: 1,222
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	G [auth A], H [auth B]	575	Salasvirus phi29	Mutation(s): 2 Gene Names: 2, gp2 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P03680 (Bacillus phage phi29) Explore P03680 Go to UniProtKB: P03680
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03680
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-d(GACTGCTTA(DOC)-3'	A [auth X], C [auth Q], F [auth J]	10	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
5'-d(ACACGTAAGCAGTC)-3'	B [auth Y], D [auth R], E [auth K]	14	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGT Query on DGT Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain NA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain NA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain NA [auth B]	NA [auth B], T [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ HAAZLUGHYHWQIW-KVQBGUIXSA-N		Interactions Focus chain NA [auth B] Focus chain T [auth A] Interactions & Density Focus chain NA [auth B] Focus chain T [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain Z [auth A] SDF format, chain YA [auth B] SDF format, chain Y [auth A] SDF format, chain XA [auth B] SDF format, chain X [auth A] SDF format, chain WA [auth B] SDF format, chain W [auth A] SDF format, chain VA [auth B] SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain Q [auth K] SDF format, chain PA [auth B] SDF format, chain P [auth K] SDF format, chain OA [auth B] SDF format, chain O [auth K] SDF format, chain N [auth R] SDF format, chain M [auth Q] SDF format, chain L [auth Y] SDF format, chain KA [auth A] SDF format, chain K [auth Y] SDF format, chain JA [auth A] SDF format, chain J [auth X] SDF format, chain IA [auth A] SDF format, chain I [auth X] SDF format, chain HA [auth A] SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CB [auth B] SDF format, chain CA [auth A] SDF format, chain BB [auth B] SDF format, chain BA [auth A] SDF format, chain AB [auth B] SDF format, chain AA [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth K] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth K] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth K] MOL2 format, chain N [auth R] MOL2 format, chain M [auth Q] MOL2 format, chain L [auth Y] MOL2 format, chain KA [auth A] MOL2 format, chain K [auth Y] MOL2 format, chain JA [auth A] MOL2 format, chain J [auth X] MOL2 format, chain IA [auth A] MOL2 format, chain I [auth X] MOL2 format, chain HA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth K] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth K] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth K] mmCIF format, chain N [auth R] mmCIF format, chain M [auth Q] mmCIF format, chain L [auth Y] mmCIF format, chain KA [auth A] mmCIF format, chain K [auth Y] mmCIF format, chain JA [auth A] mmCIF format, chain J [auth X] mmCIF format, chain IA [auth A] mmCIF format, chain I [auth X] mmCIF format, chain HA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], I [auth X], IA [auth A], J [auth X], JA [auth A], K [auth Y], KA [auth A], L [auth Y], M [auth Q], N [auth R], O [auth K], OA [auth B], P [auth K], PA [auth B], Q [auth K], QA [auth B], RA [auth B], SA [auth B], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain I [auth X] Focus chain IA [auth A] Focus chain J [auth X] Focus chain JA [auth A] Focus chain K [auth Y] Focus chain KA [auth A] Focus chain L [auth Y] Focus chain M [auth Q] Focus chain N [auth R] Focus chain O [auth K] Focus chain OA [auth B] Focus chain P [auth K] Focus chain PA [auth B] Focus chain Q [auth K] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain I [auth X] Focus chain IA [auth A] Focus chain J [auth X] Focus chain JA [auth A] Focus chain K [auth Y] Focus chain KA [auth A] Focus chain L [auth Y] Focus chain M [auth Q] Focus chain N [auth R] Focus chain O [auth K] Focus chain OA [auth B] Focus chain P [auth K] Focus chain PA [auth B] Focus chain Q [auth K] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain LA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain LA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain LA [auth B]	LA [auth B], R [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain R [auth A] Interactions & Density Focus chain LA [auth B] Focus chain R [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain MA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain MA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain MA [auth B]	MA [auth B], S [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Focus chain S [auth A] Interactions & Density Focus chain MA [auth B] Focus chain S [auth A]