PDBsum entry 1cf6

Transferase/DNA

PDB id: 1cf6

Contents

Protein chains

325 a.a.

DNA/RNA

Ligands

UCP ×2

Metals

_CR ×2

Waters ×23

Obsolete entry

PDB id:

1cf6

Name:

Transferase/DNA

Title:

Structure of DNA polymerase beta/DNA template-primer/utp phosphonate intermediate complex--potential insight into the molecular basis of fidelity

Structure:

Protein (DNA polymerase beta). Chain: a, b. Engineered: yes. DNA (5'-d(p Ap Gp Gp Cp Gp Tp Cp G)-3'). Chain: t, c. Engineered: yes. DNA (5'-d(p Cp Gp Ap Cp Gp Cp C)-3'). Chain: p, d. Engineered: yes

Source:

Rattus norvegicus. Rat. Organ: brain. Expressed in: escherichia coli. Synthetic: yes. Synthetic: yes

Resolution:

3.10Å R-factor: 0.213 R-free: 0.288

Authors:

J.W.Arndt,W.Gong,X.Zhong,Z.Lin,C.Paxson,M.D.Tsai,M.K.Chan

Key ref:

Y.R.Yuan et al. (1999). Three-dimensional structure of beta-momorcharin at 2.55 A resolution. Acta Crystallogr D Biol Crystallogr, 55, 1144-1151. PubMed id: 10329776 DOI: 10.1107/S0907444999003297

Date:

24-Mar-99 Release date: 06-Mar-00

Protein chains

P06766  (DPOLB_RAT) -  DNA polymerase beta from Rattus norvegicus

Seq: 335 a.a.

Struc: 325 a.a.

DNA/RNA chains

A-G-G-C-G-T-C-G 8 bases

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

A-G-G-C-G-T-C-G 8 bases

C-G-A-C-G-C-C 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

DNA(n) (Bound ligand (Het Group name = UCP) matches with 44.12% similarity) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

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

Added reference

DOI no: 10.1107/S0907444999003297

Acta Crystallogr D Biol Crystallogr 55:1144-1151 (1999)

PubMed id: 10329776

Three-dimensional structure of beta-momorcharin at 2.55 A resolution.

Y.R.Yuan, Y.N.He, J.P.Xiong, Z.X.Xia.

ABSTRACT

Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to Asn51. The crystal structure of beta-momorcharin has been determined using the molecular-replacement method and refined to 2. 55 A resolution. The final structural model gave an R factor of 17. 2% and root-mean-square deviations of 0.016 A and 1.76 degrees from ideal bond lengths and bond angles, respectively. beta-Momorcharin contains nine alpha-helices, two 310 helices and three beta-sheets, and its overall structure is similar to those of other single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to define the active site of beta-momorcharin as an rRNA N-glycosidase. The oligosaccharide is linked to the protein through an N-glycosidic bond, beta-GlcNAc-(1-N)-Asn51, and stretches from the surface of the N-terminal domain far from the active site, which suggests that it should not play a role in enzymatic function. The oligosaccharide of each beta-momorcharin molecule interacts with the protein through hydrogen bonds, although in the crystals most of these are intermolecular interactions with the protein atoms in an adjacent unit cell. This is the first example of an RIP structure which provides information about the three-dimensional structure and binding site of the oligosaccharide in the active chains of RIPs.

Selected figure(s)

Figure 1.
Figure 1 Stereoscopic view of the (2F[o] - F[c]) electron density of the six-stranded -sheet (molecule A) contoured at 1.0 . This diagram was prepared using the molecular-graphics program TURBO-FRODO.

Figure 5.
Figure 5 Stereoscopic diagrams of the oligosaccharide structure in [284][beta] -MMC, prepared using the molecular-graphics program TURBO-FRODO. (a) The (2F[o] - F[c]) electron density of the oligosaccharide of molecule A, contoured at 0.8 [285][sigma] . Asn51 is also shown. (b) The (2F[o] - F[c]) electron density of the oligosaccharide of molecule B, contoured at 0.8 [286][sigma] . Asn51 is also shown. (c) The superimposed oligosaccharides of molecule A (in blue) and molecule B (in red). (d) Interactions of the oligosaccharide (in blue) of molecule A with the protein. Asn51 of molecule A is shown in yellow; Glu110, Asn188-Glu189 and the C-terminus (Asn249) of molecule #A are shown in red. The N-glycosidic bond is shown as a solid line and the hydrogen bonds are shown as dashed lines. (e) Interactions of the oligosaccharide (in blue) of molecule B with the protein. Asn51 and Asn3 of molecule B are shown in yellow; Gln189 and Asn209 of molecule #B are shown in red. The N-glycosidic bond is shown as a solid line and the hydrogen bonds are shown as dashed lines.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 1144-1151) copyright 1999.

Figures were selected by an automated process.