1M5R | pdb_00001m5r

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

PDB DOI: https://doi.org/10.2210/pdb1M5R/pdb
NAKB: 1M5R

Classification: TRANSFERASE/DNA
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2002-07-10 Released: 2002-12-11
Deposition Author(s): Lariviere, L., Morera, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.224 (Depositor), 0.215 (DCC)
R-Value Work:
0.191 (Depositor), 0.183 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

A Base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition state analog

Lariviere, L., Morera, S.

(2002) J Mol Biology 324: 483-489

PubMed: 12445783 Search on PubMed
DOI: https://doi.org/10.1016/s0022-2836(02)01091-4
Primary Citation Related Structures:
1IXY, 1M5R

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.

Organizational Affiliation

Laboratoire d'Enzymologie et Biochimie Structurales, UPR 9063 CNRS, Bât. 34, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France

Macromolecule Content

Total Structure Weight: 98.88 kDa
Atom Count: 7,662
Modeled Residue Count: 754
Deposited Residue Count: 754
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA beta-glucosyltransferase	E [auth A], F [auth B]	351	Tequatrovirus T4	Mutation(s): 0 Gene Names: BGT EC: 2.4.1.27
UniProt
Find proteins for P04547 (Enterobacteria phage T4) Explore P04547 Go to UniProtKB: P04547
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04547
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(GPAPTPAPCPTP3DRPAPGPAPTPAP*G)-3'	A [auth C], C [auth D]	13	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
5'-D(CPTPAPTPCPTPGPAPGPTPAPTP*C)-3'	B [auth E], D [auth F]	13	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B]	H [auth A], I [auth A], L [auth B], M [auth B], N [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	J [auth A], O [auth B], P [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224 (Depositor), 0.215 (DCC)
R-Value Work: 0.191 (Depositor), 0.183 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83	α = 90
b = 55.9	β = 91.1
c = 99.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-12-11

Deposition Author(s):

Lariviere, L.

Morera, S.

Revision History (Full details and data files)

Version 1.0: 2002-12-11
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description