PDBsum entry 5cb1

Transferase

PDB id: 5cb1

Contents

Protein chains

326 a.a.

245 a.a.

PDB id:

5cb1

Name:

Transferase

Title:

Apo enzyme of human polymerase lambda

Structure:

DNA polymerase lambda. Chain: a, b. Fragment: unp residues 250-575. Synonym: pol lambda,DNA polymerase beta-2,pol beta2,DNA polymerase kappa. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: poll. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

3.30Å R-factor: 0.233 R-free: 0.264

Authors:

M.S.Liu,M.D.Tsai

Key ref:

M.S.Liu et al. (2016). Structural Mechanism for the Fidelity Modulation of DNA Polymerase λ. J Am Chem Soc, 138, 2389-2398. PubMed id: 26836966 DOI: 10.1021/jacs.5b13368

Date:

30-Jun-15 Release date: 24-Feb-16

Protein chain

Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda from Homo sapiens

Seq: 575 a.a.

Struc: 326 a.a.

Protein chain

Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda from Homo sapiens

Seq: 575 a.a.

Struc: 245 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B: 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: Chains A, B: E.C.4.2.99.- - ?????

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: 10.1021/jacs.5b13368

J Am Chem Soc 138:2389-2398 (2016)

PubMed id: 26836966

Structural Mechanism for the Fidelity Modulation of DNA Polymerase λ.

M.S.Liu, H.Y.Tsai, X.X.Liu, M.C.Ho, W.J.Wu, M.D.Tsai.

ABSTRACT

The mechanism of DNA polymerase (pol) fidelity is of fundamental importance in chemistry and biology. While high-fidelity pols have been well studied, much less is known about how some pols achieve medium or low fidelity with functional importance. Here we examine how human DNA polymerase λ (Pol λ) achieves medium fidelity by determining 12 crystal structures and performing pre-steady-state kinetic analyses. We showed that apo-Pol λ exists in the closed conformation, unprecedentedly with a preformed MgdNTP binding pocket, and binds MgdNTP readily in the active conformation in the absence of DNA. Since prebinding of MgdNTP could lead to very low fidelity as shown previously, it is attenuated in Pol λ by a hydrophobic core including Leu431, Ile492, and the Tyr505/Phe506 motif. We then predicted and demonstrated that L431A mutation enhances MgdNTP prebinding and lowers the fidelity. We also hypothesized that the MgdNTP-prebinding ability could stabilize a mismatched ternary complex and destabilize a matched ternary complex, and provided evidence with structures in both forms. Our results demonstrate that, while high-fidelity pols follow a common paradigm, Pol λ has developed specific conformations and mechanisms for its medium fidelity. Structural comparison with other pols also suggests that different pols likely utilize different conformational changes and microscopic mechanisms to achieve their catalytic functions with varying fidelities.