1IXY

Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex

Summary for 1IXY

• Entry DOI: 10.2210/pdb1ixy/pdb
• Related: 1JG6 1M5R
• Descriptor: 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3', 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3', DNA beta-glucosyltransferase, ... (7 entities in total)
• Functional Keywords: protein-dna complex, base-flipping, abasic site, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage T4
• Total number of polymer chains: 6
• Total formula weight: 98339.78

Authors

Lariviere, L.,Morera, S. (deposition date: 2002-07-09, release date: 2002-12-04, Last modification date: 2023-08-16)

Primary citation

Lariviere, L.,Morera, S.
A Base-flipping Mechanism for the T4 Phage beta-Glucosyltransferase and Identification of a Transition-state Analog
J.Mol.Biol., 324:483-490, 2002

PubMed Abstract: T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment containing an abasic site. We obtained two crystal structures of a ternary complex BGT-UDP-DNA at 1.8A and 2.5A resolution, one with a Tris molecule and the other with a metal ion at the active site. Both structures reveal a large distortion in the bound DNA. BGT flips the deoxyribose moiety at the abasic site to an extra-helical position and induces a 40 degrees bend in the DNA with a marked widening of the major groove. The Tris molecule mimics the glucose moiety in its transition state. The base-flipping mechanism, which has so far been observed only for glycosylases, methyltransferases and endonucleases, is now reported for a glucosyltransferase. BGT is unique in binding and inserting a loop into the DNA duplex through the major groove only. Furthermore, BGT compresses the backbone DNA one base further than the target base on the 3'-side.

PubMed: 12445783
DOI: 10.1016/S0022-2836(02)01091-4

Experimental method

X-RAY DIFFRACTION (2.5 Å)