PDBsum entry 1s5j

Transferase

PDB id: 1s5j

Contents

Protein chain

727 a.a. *

Ligands

SO4 ×9

Metals

_MG

Waters ×248

* Residue conservation analysis

PDB id:

1s5j

Name:

Transferase

Title:

Insight in DNA replication: the crystal structure of DNA polymerase b1 from the archaeon sulfolobus solfataricus

Structure:

DNA polymerase i. Chain: a. Engineered: yes

Source:

Sulfolobus solfataricus. Organism_taxid: 2287. Strain: mt 4. Gene: dpo1, pols, sso0552. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.40Å R-factor: 0.234 R-free: 0.272

Authors:

C.Savino,L.Federici,V.Nastopoulos,K.A.Johnson,F.M.Pisani,M.Rossi, D.Tsernoglou

Key ref:

C.Savino et al. (2004). Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus. Structure, 12, 2001-2008. PubMed id: 15530364 DOI: 10.1016/j.str.2004.09.007

Date:

21-Jan-04 Release date: 09-Nov-04

Protein chain

P26811  (DPOL1_SULSO) -  DNA polymerase 1 from Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

Seq: 882 a.a.

Struc: 727 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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

Added reference

DOI no: 10.1016/j.str.2004.09.007

Structure 12:2001-2008 (2004)

PubMed id: 15530364

Insights into DNA replication: the crystal structure of DNA polymerase B1 from the archaeon Sulfolobus solfataricus.

C.Savino, L.Federici, K.A.Johnson, B.Vallone, V.Nastopoulos, M.Rossi, F.M.Pisani, D.Tsernoglou.

ABSTRACT

To minimize the large number of mispairs during genome duplication owing to the large amount of DNA to be synthesized, many replicative polymerases have accessory domains with complementary functions. We describe the crystal structure of replicative DNA polymerase B1 from the archaeon Sulfolobus solfataricus. Comparison between other known structures indicates that although the protein is folded into the typical N-terminal, editing 3'-5'exonuclease, and C-terminal right-handed polymerase domains, it is characterized by the unusual presence of two extra alpha helices in the N-terminal domain interacting with the fingers helices to form an extended fingers subdomain, a structural feature that can account for some functional features of the protein. We explore the structural basis of specific lesion recognition, the initial step in DNA repair, describing how the N-terminal subdomain pocket of archaeal DNA polymerases could allow specific recognition of deaminated bases such as uracil and hypoxanthine in addition to the typical DNA bases.

Selected figure(s)

Figure 4.
Figure 4. Modeling Deminated Bases into the Protein(A) Uridine5'monophosphate (dUMP). It is possible to see the binding between the R142 and the sulfate ion that mimics the phosphate in the 5' position, the hydrogen bonds that fix the position of R464 and N161 and would be expected to discriminate between oxygen or amino group, i.e., uracil or cytosine base, and the position of Y158, which could contribute to steric discrimination against the thymine methyl group.(B) Hypoxanthine. The oxygen in position 6 on hypoxanthine could be recognized in same way as the oxygen in position 4 of uracil. Only the hypoxanthine nucleoside is shown to highlight the position of the sulfate ion. The dUMP and the hypoxanthine were positioned manually to maximize hydrogen bonding and minimize steric clashes.

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 2001-2008) copyright 2004.

Figure was selected by an automated process.