PDBsum entry 1xsl

Transferase/DNA

PDB id: 1xsl

Contents

Protein chains

327 a.a. *

DNA/RNA

Ligands

CAC

Metals

_MG ×3

_NA ×6

Waters ×843

* Residue conservation analysis

PDB id:

1xsl

Name:

Transferase/DNA

Title:

Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap

Structure:

5'-d( Cp Gp Gp Cp Ap Gp Cp Gp Cp Ap C)-3'. Chain: b, f, j, n. Engineered: yes. 5'-d( Gp Tp Gp Cp Gp C)-3'. Chain: c, g, k, o. Engineered: yes. 5'-d(p Gp Cp Cp G)-3'. Chain: d, h, l, p. Engineered: yes.

Source:

Synthetic: yes. Other_details: template DNA. Other_details: primer DNA. Other_details: downstream primer DNA. Homo sapiens. Human. Organism_taxid: 9606. Gene: poll. Expressed in: escherichia coli.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.30Å R-factor: 0.207 R-free: 0.252

Authors:

M.Garcia-Diaz,K.Bebenek,J.M.Krahn,T.A.Kunkel,L.C.Pedersen

Key ref:

M.Garcia-Diaz et al. (2005). A closed conformation for the Pol lambda catalytic cycle. Nat Struct Mol Biol, 12, 97-98. PubMed id: 15608652 DOI: 10.1038/nsmb876

Date:

19-Oct-04 Release date: 18-Jan-05

Protein chains

Q9UGP5  (DPOLL_HUMAN) -  DNA polymerase lambda from Homo sapiens

Seq: 575 a.a.

Struc: 327 a.a.

DNA/RNA chains

C-G-G-C-A-G-C-G-C-A-C 11 bases

G-T-G-C-G-C 6 bases

G-C-C-G 4 bases

C-G-G-C-A-G-C-G-C-A-C 11 bases

G-T-G-C-G-C 6 bases

G-C-C-G 4 bases

C-G-G-C-A-G-C-G-C-A-C 11 bases

G-T-G-C-G-C 6 bases

G-C-C-G 4 bases

C-G-G-C-A-G-C-G-C-A-C 11 bases

G-T-G-C-G-C 6 bases

G-C-C-G 4 bases

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.- - ?????

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: 10.1038/nsmb876

Nat Struct Mol Biol 12:97-98 (2005)

PubMed id: 15608652

A closed conformation for the Pol lambda catalytic cycle.

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen.

ABSTRACT

Pol lambda is a family X member believed to fill short gaps during DNA repair. Here we report crystal structures of Pol lambda representing three steps in filling a single-nucleotide gap. These structures indicate that, unlike other DNA polymerases, Pol lambda does not undergo large subdomain movements during catalysis, and they provide a clear characterization of the geometry and stereochemistry of the in-line nucleotidyl transfer reaction.

Selected figure(s)

Figure 1.
Figure 1. Superimposition of the Pol structures. (a) The C traces of the binary (dark gray), nick ternary (green) and precatalytic ternary (orange) structures reveal two differences. One involves -strand 8 (ref. 10) (labeled A). The second involves -strands 3 and 4 (B; see text). Black lines indicate the span of the different subdomains: 8 kDa domain (8), fingers (F), palm (P) and thumb (T). (b) DNA shift upon dNTP binding. The DNA and part of the palm subdomain is shown for the binary (blue) and precatalytic ternary complex (yellow-brown). Hydrogen bonds, dashed lines; Mg2+ ion observed in the structure of the ternary complex, green.

Figure 2.
Figure 2. Conformational changes and nucleotidyl transfer catalysis. (a) Stereo representation of an overlay of the Pol active site in the binary (gray) and precatalytic ternary (brown) complex structures, focusing on the side chain movements observed upon dNTP binding. Hydrogen bonds, dashed lines. (b) Stereo view of the postcatalytic ternary complex. The two last bases of the primer strand and the catalytic carboxylates are shown, together with the pyrophosphate molecule. An overlay of the equivalent atoms in the structure of the precatalytic ternary complex is transparent. The line of transfer, dashed line. The 3' O that was the acceptor in the reaction (3'O[N]), the bridging oxygen of the leaving group (O[L]) and the phosphate (P ) are labeled.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 97-98) copyright 2005.