PDBsum entry 2fln

Replication/DNA

PDB id: 2fln

Contents

Protein chain

366 a.a. *

DNA/RNA

Waters ×101

* Residue conservation analysis

PDB id:

2fln

Name:

Replication/DNA

Title:

Binary complex of catalytic core of human DNA polymerase iota with DNA (template a)

Structure:

DNA template strand. Chain: t. Engineered: yes. DNA primer strand. Chain: p. Engineered: yes. DNA polymerase iota. Chain: a. Synonym: rad30 homolog b, eta2.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: poli, rad30b. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.

Biol. unit:

Hexamer (from PDB file)

Resolution:

2.50Å R-factor: 0.231 R-free: 0.279

Authors:

D.T.Nair,R.E.Johnson,L.Prakash,S.Prakash,A.K.Aggarwal

Key ref:

D.T.Nair et al. (2006). An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site. Structure, 14, 749-755. PubMed id: 16615915 DOI: 10.1016/j.str.2006.01.010

Date:

06-Jan-06 Release date: 05-Dec-06

Protein chain

Q9UNA4  (POLI_HUMAN) -  DNA polymerase iota from Homo sapiens

Seq: 740 a.a.

Struc: 366 a.a.

DNA/RNA chains

T-A-G-G-G-T-C-C-T 9 bases

A-G-G-A-C-C-DOC 7 bases

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.2006.01.010

Structure 14:749-755 (2006)

PubMed id: 16615915

An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site.

D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal.

ABSTRACT

Substrate-induced conformational change of the protein is the linchpin of enzymatic reactions. Replicative DNA polymerases, for example, convert from an open to a closed conformation in response to dNTP binding. Human DNA polymerase-iota (hPoliota), a member of the Y family of DNA polymerases, differs strikingly from other polymerases in its much higher proficiency and fidelity for nucleotide incorporation opposite template purines than opposite template pyrimidines. We present here a crystallographic analysis of hPoliota binary complexes, which together with the ternary complexes show that, contrary to replicative DNA polymerases, the DNA, and not the polymerase, undergoes the primary substrate-induced conformational change. The incoming dNTP "pushes" templates A and G from the anti to the syn conformation dictated by a rigid hPoliota active site. Together, the structures posit a mechanism for template selection wherein dNTP binding induces a conformational switch in template purines for productive Hoogsteen base pairing.

Selected figure(s)

Figure 3.
Figure 3. Comparison of the hPolι Active Site in Binary and Ternary Complexes
(A) Top: close-up views of the hPolι active site region in hPolι[A] binary (left) and hPolι[A.dTTP] ternary (right) complexes. The fingers and palm domains and the PAD are shown in yellow, blue, and green, respectively. The DNA is colored gray, and the template dA and incoming dTTP are shown in red. The putative Mg^2+ ions in the ternary complex are shown in dark blue. The catalytic residues (D34, D126, and E127), the residues apposed close to template dA (Q59, K60, L62, V64, L78, S307, K309, and R347), and incoming dTTP (Y39, T65, Y68, R71, and K214) are highlighted and labeled. Note that template dA is in the anti conformation in the binary complex but flips to the syn conformation in the ternary complex. Note also that some of the amino acids, including Leu62, Val64, and Arg71, change conformation in response to dTTP binding. Bottom: simulated annealing F[o] − F[c] omit maps (contoured at 3.0σ) showing template dA in the anti conformation in the binary complex (left) and in the syn conformation in the ternary complex (right). In the ternary complex, dA makes a Hoogsteen base pair with incoming dTTP, which remains in the anti conformation.
(B) Top: close-up views of the hPolι active site region in hPolι[G] binary (left) and hPolι[G.dCTP] ternary (right) complexes. Note that template dG is in the anti conformation in the binary complex but flips to the syn conformation in the ternary complex. Bottom: simulated annealing F[o] − F[c] omit maps (contoured at 3.0σ) showing template dG in the anti conformation in the binary complex (left) and in the syn conformation in the ternary complex (right). In the ternary complex, dG makes a Hoogsteen base pair with incoming dCTP, which remains in the anti conformation and is likely protonated. Figure 3. Comparison of the hPolι Active Site in Binary and Ternary Complexes(A) Top: close-up views of the hPolι active site region in hPolι[A] binary (left) and hPolι[A.DTTP] ternary (right) complexes. The fingers and palm domains and the PAD are shown in yellow, blue, and green, respectively. The DNA is colored gray, and the template dA and incoming dTTP are shown in red. The putative Mg^2+ ions in the ternary complex are shown in dark blue. The catalytic residues (D34, D126, and E127), the residues apposed close to template dA (Q59, K60, L62, V64, L78, S307, K309, and R347), and incoming dTTP (Y39, T65, Y68, R71, and K214) are highlighted and labeled. Note that template dA is in the anti conformation in the binary complex but flips to the syn conformation in the ternary complex. Note also that some of the amino acids, including Leu62, Val64, and Arg71, change conformation in response to dTTP binding. Bottom: simulated annealing F[o] − F[c] omit maps (contoured at 3.0σ) showing template dA in the anti conformation in the binary complex (left) and in the syn conformation in the ternary complex (right). In the ternary complex, dA makes a Hoogsteen base pair with incoming dTTP, which remains in the anti conformation.(B) Top: close-up views of the hPolι active site region in hPolι[G] binary (left) and hPolι[G.DCTP] ternary (right) complexes. Note that template dG is in the anti conformation in the binary complex but flips to the syn conformation in the ternary complex. Bottom: simulated annealing F[o] − F[c] omit maps (contoured at 3.0σ) showing template dG in the anti conformation in the binary complex (left) and in the syn conformation in the ternary complex (right). In the ternary complex, dG makes a Hoogsteen base pair with incoming dCTP, which remains in the anti conformation and is likely protonated.

Figure 4.
Figure 4. anti versus syn Conformation
Templates dA and dG are in the anti (binary) conformation in the absence of incoming dNTP (left), but they rotate about their glycosidic bond to the syn (ternary) conformation in response to dNTP binding (right). Figure 4. anti versus syn ConformationTemplates dA and dG are in the anti (binary) conformation in the absence of incoming dNTP (left), but they rotate about their glycosidic bond to the syn (ternary) conformation in response to dNTP binding (right).

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 749-755) copyright 2006.

Figures were selected by an automated process.