PDBsum entry 3b0x

Transferase

PDB id: 3b0x

Contents

Protein chain

575 a.a.

Ligands

DGT

Metals

_ZN ×2

_CA ×4

_CL

Waters ×551

PDB id:

3b0x

Name:

Transferase

Title:

K263a mutant of polx from thermus thermophilus hb8 complexed with ca- dgtp

Structure:

DNA polymerase beta family (x family). Chain: a. Engineered: yes. Mutation: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: polx, ttha1150. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.36Å R-factor: 0.172 R-free: 0.198

Authors:

S.Nakane,N.Nakagawa,R.Masui,S.Kuramitsu,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

S.Nakane et al. (2012). The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. J Mol Biol, 417, 179-196. PubMed id: 22306405

Date:

17-Jun-11 Release date: 02-May-12

Protein chain

Q5SJ64  (Q5SJ64_THET8) -  DNA polymerase beta from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 575 a.a.

Struc: 575 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• 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

J Mol Biol 417:179-196 (2012)

PubMed id: 22306405

The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.

S.Nakane, H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui.

ABSTRACT

No abstract given.