PDBsum entry 5j2c

Transferase/DNA

PDB id

5j2c

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Contents

			Protein chain

					326 a.a.

			DNA/RNA

			Ligands

					DUP

			Metals

					_CL ×4


					_MG ×2


					_NA ×2

			Waters ×328

PDB id:

5j2c

Links

Name:

Transferase/DNA

Title:

Ternary complex crystal structure of DNA polymerase beta with c:a mismatch at the primer terminus

Structure:

DNA polymerase beta. Chain: a. Engineered: yes. Template strand. Chain: t. Engineered: yes. Primer strand. Chain: p. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

2.10Å

R-factor:

0.212

R-free:

0.266

Authors:

V.K.Batra,S.H.Wilson

Key ref:

V.K.Batra et al. (2016). Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure, 24, 1863-1875. PubMed id: 27642161 DOI: 10.1016/j.str.2016.08.006

Date:

29-Mar-16

Release date:

26-Oct-16

PROCHECK

	Headers

	References

Protein chain

P06746 (DPOLB_HUMAN) - DNA polymerase beta from Homo sapiens

Seq: Struc:					335 a.a. 326 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DNA/RNA chains

		C-C-G-A-C-A-C-C-G-C-A-T-C-A-G-C 16 bases
		G-C-T-G-A-T-G-C-G-A 10 bases
		G-T-C-G-G 5 bases



		Enzyme reactions

Enzyme class 1:

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

Enzyme class 2:

E.C.4.2.99.- - ?????

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

Enzyme class 3:

E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.

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

Reaction:

2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1016/j.str.2016.08.006	Structure 24:1863-1875 (2016)
PubMed id: 27642161

Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.
V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson.

ABSTRACT

No abstract given.